The "Fire Sale" offseason

Following the World Series victory, Huizenga dismantled the team, claiming financial losses despite winning the World Series. He traded most of the club's best players in one of the biggest fire sales in sports history. The first deal came days after the World Series, when outfielder Moisés Alou was traded to the Houston Astros for pitchers Oscar Hernandez and Manuel Barrios. The Marlins then traded Kevin Brown to the San Diego Padres for Derrek Lee and 2 minor leaguers. Finally, in May 1998, they dealt Bobby Bonilla, Gary Sheffield, Charles Johnson, Jim Eisenreich, and Manuel Barrios to the Los Angeles Dodgers for Mike Piazza and Todd Zeile, both of whom would be gone via trades by midseason. On the flip side, these trades brought promising youngsters Derrek Lee and A. J. Burnett.

The Marlins did manage to win a second World Series just six years later in 2003. One player played on both championship teams despite being included in the "fire sale": Jeff Conine. Conine was traded after the 1997 season to the Kansas City Royals who in turn traded him to the Baltimore Orioles. The Marlins picked up Conine in a late season trade during the 2003 pennant race.

2003: Second World Series victory

During the offseason, the Marlins signed free agent catcher Iván Rodríguez – a 10-time Gold Glove Award winner – and acquired speedy outfielder Juan Pierre from the Colorado Rockies hoping to offset the loss of sluggers Cliff Floyd and Preston Wilson. The Marlins did acquire P Mike Hampton but dealt him and his hefty contract to the Braves for P Tim Spooneybarger.

The Marlins struggled in the opening stages of the season, going 16–22. During that span, Florida lost its top three pitchers: A. J. Burnett, Josh Beckett, and Mark Redman. On May 11, Florida replaced manager Jeff Torborg with 72-year-old Jack McKeon. On May 22, the Marlins hit bottom with a major league worst record of 19–29, having lost 6 straight games. However, help was on the way.

On May 9, the Marlins called up high-kicking southpaw Dontrelle Willis from the Double-A Carolina Mudcats and helped carry the injury-plagued Marlins with an 11–2 record in his first 17 starts. Miguel Cabrera (also from the Mudcats) filled in well, hitting a walk off home run in his first major league game, against the Tampa Bay Devil Rays at Pro Player Stadium. Both Willis and Cabrera would later prove to be essential parts of the Marlin's playoff success. Jeff Conine – an original Marlin and member of the 1997 World Series team – returned from Baltimore, and closer Ugueth Urbina arrived from the Texas Rangers. These acquisitions helped to keep the team in contention, and although they finished ten games behind the Braves, the Marlins captured the NL wild card.

The Marlins won the Division Series against the favored San Francisco Giants three games to one. The series ended with a dramatic collision between Marlins catcher Rodríguez and Giants first baseman J. T. Snow, making it the first postseason series ever to end with the potential tying run being thrown out at the plate. It was the second time that the Marlins defeated the Giants in the Division Series, having done so in 1997.

On October 15, the Marlins defeated the Chicago Cubs four games to three in the Championship Series, coming back from a three games to one deficit. A Beckett complete-game shutout in Game 5 kept the Marlins alive. Game 6 saw the Marlins play a role in one of baseball's most infamous moments: "The Inning" . With 1 one out in the 8th inning and the Cubs 3 runs ahead, Marlins 2nd baseman Luis Castillo hit a pop foul a row into the stands along the third base line. Cubs fan Steve Bartman reached for the ball, preventing Cubs LF Moisés Alou from making the out and setting off an 8-run Marlins rally. The incident with Steve Bartman and a come-from-behind win in Wrigley Field in Game 7 helped the Marlins capture their second NL pennant, keeping the "Curse of the Billy Goat" alive and well.

In the 2003 World Series, the Marlins defeated the heavily favored New York Yankees in six games, winning the sixth game in Yankee Stadium. Shortstop Álex González helped the Marlins in Game 4 of the series with a walk off home run in extra innings. Josh Beckett was named the Most Valuable Player for the series after twirling a five-hit complete-game shutout in Game 6. Skipper Jack McKeon became the oldest manager ever to win a World Series title. The Marlins became the first opposing team to win a Series championship on the field at Yankee Stadium since 1981, when the Los Angeles Dodgers did it. The Marlins are also the last team to win a World Series at the original Yankee Stadium; the Yankees themselves would not participate in another World Series until 2009, when they defeated the then-defending champion Philadelphia Phillies at the new Yankee Stadium. The Marlins won the series despite scoring fewer runs (17) than the Yankees (21).

2004: Winning season, but no repeat

The offseason after their second World Series title, the Marlins made a questionable cost-cutting move as Derrek Lee was traded to Chicago Cubs for Hee-seop Choi and pitcher Mike Nannini. The Marlins also lost key parts of their second championship team, Ugueth Urbina and Iván Rodríguez left via free agency (signed by the Detroit Tigers). Marlins third base coach Ozzie Guillén also departed to be manager of the Chicago White Sox. The Marlins did get good news though as Dontrelle Willis was named NL Rookie of the Year and Jack McKeon named Manager of the Year. They also signed Mike Lowell to a new four-year contract.

After winning the 2003 World Series, the Marlins entered 2004 with high hopes and a retooled roster. Retaining a core of stars from their title team and hoping that newly acquired 1B Hee-seop Choi would emerge, the Marlins fell short of reaching the postseason, but they posted the third winning season in franchise history, boasting an 83–79 record. During the season, the Marlins were to make one of the biggest trades in club history as Los Angeles got P Brad Penny, 1B Choi and Double-A left-hander Bill Murphy in exchange for P Guillermo Mota, C Paul Lo Duca and OF Juan Encarnación. Pitchers Carl Pavano and Armando Benítez turned in record-setting performances. Pavano went 18–8 with a 3.30 ERA, and his 18 wins established a season high by a Marlin. Benitez became the club's season saves leader with 47 (in 51 saves attempts). Pavano, Benitez, Mike Lowell and Miguel Cabrera each enjoyed All-Star seasons, with Cabrera belting 33 homers (second-most ever in a season by a Marlin) while driving in 112 runs.

2005

2006: Rebuilding

At the start of the year, the Marlins had a team salary close to $21 million. Not only was it the lowest team salary in all of MLB, but New York Yankees third baseman Alex Rodriguez alone made more money than the entire Marlins team. The Marlins made MLB history when they started six rookies in their Opening Day lineup.^[14] Sporting the league's youngest team, the Marlins were predicted before the season to lose more than 100 games. Instead, the youthful squad greatly exceeded expectations, often in historical fashion. After getting off to an 11–31 start, the Marlins found themselves at 73–72 on September 12, making them the first team in the modern baseball era to improve to better than .500 after being as much as 20 games under .500. Also, for the first time in MLB history, four rookies topped double digits in wins: Josh Johnson, Scott Olsen, Ricky Nolasco and Aníbal Sánchez.

On September 6, 2006, Sanchez threw the fourth no-hitter in franchise history, beating Arizona, 2–0, at Dolphin Stadium. Miguel Cabrera finished second in the N.L. in batting average, and set a franchise season mark with his .339 average. Dan Uggla became the first Rule 5 pick to be selected to the All-Star Game in the season in which he was drafted and won Sporting News Rookie of the Year for the National League and won the Players' Choice award as the league's most outstanding rookie. Hanley Ramírez won the N.L. Rookie of the Year Award, and Joe Girardi was voted N.L. Manager of the Year. Dan Uggla finished third in the voting and starting pitcher Josh Johnson, fourth; starting pitchers Scott Olsen and Aníbal Sánchez and left fielder Josh Willingham received one third-place vote each.

Additionally, the Marlins had four of their rookie starting pitchers (Aníbal Sánchez, Josh Johnson, Scott Olsen, and Ricky Nolasco) win at least ten games, becoming the first team in major-league history to do so. The 2006 Marlins also had five ten-game winners for the first time in franchise history (including Dontrelle Willis).

Shortly after the 2006 season ended and following months of speculation, Marlins manager Joe Girardi was fired on October 3, 2006, not long after winning the National League Manager of the Year award. This was due to a game against the Los Angeles Dodgers earlier in the year in which Girardi did not challenge a call that pitcher Taylor Tankersley thought was a strike and this prompted owner Jeffrey Loria, who was in the stands and a few feet away from the dugout, to call out Girardi who refused to listen to him. This was not the only thing that triggered the feud; earlier in the year Girardi reportedly wanted 1B Mike Jacobs to start off the year in triple A, Willingham to start at catcher, Miguel Cabrera to start at first base.^[15] Within hours, Atlanta Braves third base coach Fredi González was named his replacement and was signed to a three-year contract.

2007: Injuries deplete the Fish

After a 2006 season which saw them defy expectations time and again, the Marlins entered 2007 hanging on to the belief that they could compete with anyone. It did not turn out that way. Injuries ravaged the starting rotation and the Marlins struggled all season, ultimately finishing in last place in the National League East for the first time since 1999. Josh Johnson underwent Tommy John surgery and Aníbal Sánchez had right shoulder surgery. Ricky Nolasco dealt with a sore elbow all season. Suddenly, the strength of the team—the starting rotation—was minus three key players. Despite a disappointing finish, there certainly were a number of highs—Kevin Gregg emerged as a dominant closer, Hanley Ramírez developed into a legitimate superstar and Miguel Cabrera proved why he already was one—but none of them could ultimately overcome the odds heavily stacked against the Marlins. On the downside, southpaws Dontrelle Willis and Scott Olsen had disappointing campaigns. What was encouraging was an otherwise disappointing season ended on a high note. The team won five of six to end the season (sweeping the Cubs and taking two of three with the Mets at Shea Stadium). Still, after the season, the franchise went in a different direction. The year was capped by the trading of their two biggest stars, slugger Miguel Cabrera and pitcher Dontrelle Willis. Talks with both the Los Angeles Angels and San Francisco Giants fell apart. On December 5, 2007, the Marlins agreed to the terms of a trade with the Detroit Tigers. The trade would surprisingly send not only Cabrera, but also Willis, to the Tigers. In return, the Marlins did not receive four players, but six. The Marlins received center fielder Cameron Maybin, catcher Mike Rabelo, and pitchers Andrew Miller, Eulogio De La Cruz, Burke Badenhop, and Dallas Trahern.

The Marlins did have some bright spots on offense as they set club records for runs scored (790), hits (1,504), doubles (340), home runs (201), RBIs (749) and slugging percentage (.448). As the Marlins wrapped up the season they announced that pitching coach Rick Kranitz would not be back with the club and extended Larry Beinfest and Michael Hill to long-term deals that run through 2015 along with promotions to President of Baseball Operations and Vice President/General Manager, respectively.,^[16][17]

2008: Back to .500 baseball

The Marlins began 2008 on a positive note. Analysts expected a lackluster performance on the field, citing the low payroll and loss of Dontrelle Willis and Miguel Cabrera during the offseason. However, the Marlins got off to one of the best starts in team history. At one point the Marlins were 30–20, the first time since September 14, 2005, the team had been 10 games over .500. They jumped atop of the National League East in April and May, the first time since 2002 that they held the lead that late in the season. The good start was attributed to powerful offensive production from their core of Mike Jacobs, Hanley Ramírez, Dan Uggla, Josh Willingham, and Jorge Cantú and quality pitching by southpaw Scott Olsen and right-hander Ricky Nolasco. The Marlins' hot start made them a rare buyer at the July trade deadline, where they were involved in talks on a three-way deal with the Pittsburgh Pirates and Boston Red Sox which could have brought Manny Ramírez to South Florida. The Marlins backed out at the last second when trade talks turned to their coveted power-hitting prospect, Giancarlo Stanton. Instead, Manny Ramírez ended up with the Dodgers and the Marlins wound up trading for Arthur Rhodes.

The team also received encouraging news when injured pitcher Josh Johnson made a fast recovery from Tommy John surgery and Aníbal Sánchez came back from a torn labrum in the shoulder, both leaping into the rotation right away along with newly called up prized prospect Chris Volstad. In addition, the Marlins sent two players, Hanley Ramírez, who started the game at shortstop, and reserve Dan Uggla to the last All-Star Game at Yankee Stadium. The Marlins signed Hanley Ramírez to a 6-year, $70 million deal, making him the richest Marlin in history.

The team struggled in the month of August, when they went 11–16 due to lack of the offense they had in the early part of the season. In September, the Marlins rallied with a nine-game winning streak, tying the franchise record, thanks in part to prized prospect, Cameron Maybin. However they lost four straight afterwards and were eliminated from playoff contention, although but they did manage to eliminate the New York Mets for the second consecutive season on the final day, winning the final game at Shea Stadium, 4–2.

The team finished with a franchise record for most home runs in a season at 208. Mike Jacobs, Dan Uggla, Hanley Ramírez and Jorge Cantú made MLB history by becoming the first foursome of infielders to hit at least 25 homers in a season. Just a day after the World Series concluded, the Marlins began wheeling and dealing. They traded first baseman Mike Jacobs to the Royals for reliever Leo Núñez, who the Marlins hoped could become a setup-man in late innings. A few weeks later, the Marlins traded power hitting outfielder Josh Willingham and southpaw Scott Olsen to the Nationals for utility player Emilio Bonifacio and two minor leaguers. Soon after the Marlins traded closer Kevin Gregg to the Cubs for relief prospect José Ceda.

2009: Falling short

A few weeks before the regular season, the Florida Marlins' 15-year quest for a permanent home became a reality by agreeing to bankroll a big share of a $634 million stadium complex to rise on the grounds of the old Orange Bowl site. The Marlins hoped to open at the new stadium on Opening Day 2012 with a new name of Miami Marlins.

The Marlins kicked off the new season with the youngest team in baseball and with the lowest payroll for the fourth consecutive season. New leadoff man Emilio Bonifacio stole the show on Opening Day. He hit the first Opening Day inside-the-park home run since Carl Yastrzemski did it for the Boston Red Sox in 1968 and had three stolen bases to go along with four hits. Hanley Ramírez hit his first career grand slam as the Marlins went on to score 12 runs, the most ever in franchise history on Opening Day.

The Marlins started the 2009 season hot by sweeping the Washington Nationals, only the second time they started the season with sweep since the 1997 Marlins team. The Marlins won their first four games for the first time in franchise history and started 11–1, which included 2 out of 3 wins from the Mets, the first Marlins franchise sweep at Turner Field, and three comeback late-inning wins against the Nationals in Washington, sweeping the teams' second series matchup. The 11–1 start was the best start in Marlins history. They then lost their next seven games starting with the 62–99 Pittsburgh Pirates making them the first team in NL history to win seven straight games then lose the next seven. But even though they were below .500 by as many as five games, they rebounded to 2 games above .500 as of July 1, 2009. Cody Ross, the leader of the rebound, hit 2 grand slams in 2 weeks. The Marlins also amazed many in the final series before the All-Star break against the Arizona Diamondbacks. Originally trailing by seven runs after five innings, the Marlins entered the eighth inning down 7–4, they sent 14 batters to the plate. In the benchmark frame, they collected eight hits, and had eight different players score for a total of ten runs in the inning. In all the Marlins collected 14 unanswered runs as they came back for their 21st come from behind victory of the season. After the first 100 games of the season they stood second in the NL East with a record of 52–48.

Coming out of the All-Star break, the Marlins were swept in three games by the Phillies, but they responded by sweeping the Padres in San Diego before taking two of three against the Dodgers. That 5–1 West Coast road trip—from July 20–26—reinforced to management that the team was in contention. Instead of being sellers at the July 31 non-waiver trade deadline, first baseman Nick Johnson was acquired from the Nationals for pitching prospect Aaron Thompson, in the hopes that Johnson would bring his renowned plate discipline to the forefront of the Marlins' lineup. However other rumors began to surface that the team was exploring options in deals that would bring major players to Florida, including superstars Roy Halladay and Adrián González, as well as closer Heath Bell.

In August, the Marlins offense would take off. Rookie Chris Coghlan set a club record with ten consecutive multihit games. In addition, the Marlins would set a team record with 14 consecutive games with 10 or more hits, becoming the first team since the 1937 St. Louis Browns to reach that milestone.^[18][19] August would also see the Marlins sweeping the division leading Philadelphia Phillies after getting swept by the division cellar Washington Nationals. In light of being in the playoff race, the Marlins were rumored to have been targeting veteran pitchers John Smoltz and ex-Marlin Brad Penny.^[20][21] The Marlins ended the 2009 Season with their 3rd best record in franchise history, 87–75, topped only by the 1997 (92 wins) and 2003 (91) World Series championship teams. However, the status of Fredi González for the 2010 season was put in question when a report by ESPN's Buster Olney said the Marlins had made contact with Bobby Valentine. The Marlins put those rumors to rest days later confirming that the all-time winningest manager in franchise history would remain at the helm. On the other hand, pitching coach Mark Wiley and infield/first-base coach Andy Fox were not retained.

Soon after the World Series, the Marlins began their off-season. On November 5, Jeremy Hermida was dealt to the Boston Red Sox in exchange for two prospects, pitchers Hunter Jones and José Álvarez. The team also saw a higher number of awards handed out to the team, as Ramirez notched his second straight Silver Slugger award, and Chris Coghlan was named the National League Rookie of the Year. Miami native and Marlins' Special Assistant to the President Andre Dawson was elected by the eligible members of the Baseball Writers' Association of America to the 2010 Class of the Baseball Hall of Fame. Dawson played with the Marlins in his final two seasons (1995 & 1996)^[22] The Marlins were also active on the international front, targeting and offering Cuban defector Aroldis Chapman a five-year offer worth $16 million, but lost out to the Cincinnati Reds, who signed the heralded lefty for $30 million for over six years.^[23]

2010: Rookie emergence

The Marlins announced in a statement on January 5, 2010, in preparation for the move to the new ballpark and name change, that the Marlins road jersey would no longer bear the name "Florida" on the front. Also the "F" marlin sleeve patch would no longer be on the jersey.^[24]

On January 12, 2010, as part of an agreement between Major League Baseball and the players' union, the Marlins agreed to increase payroll in line with the money it receives each year from revenue sharing. It could have meant that the Marlins would be more inclined to hang on to All-Star second baseman Dan Uggla rather than trade him as they had been trying to do for several months.^[25] A few days after agreeing with MLB to increase payroll, the Marlins signed their ace right-hander, Josh Johnson to a four-year deal worth $39 million, the second biggest contract ever for a pitcher heading into his second salary arbitration year. The only bigger deal was signed by Johan Santana, then of the NY Mets, for $40 million over four years. The deal locked up the team's pitching ace beyond the opening of the new stadium in 2012, along with Hanley Ramírez.^[26] Not too long after the deal, the Marlins avoided arbitration with all-star second baseman Dan Uggla by signing a one-year, $7.8 million deal which was the third-highest single season total in franchise history behind Iván Rodríguez's $10 million in 2003 and Gary Sheffield's $14.9 million in 1998.^[27]

Coming out of spring training, there were playoff aspirations for the Marlins, which had held the same nucleus since 2006 despite the fact they had the National League's third-lowest payroll. Marlins owner Jeffrey Loria expressed high hopes saying, "I expect us to make the playoffs, we've got all the ammunition we need."

However, those aspirations proved to be misplaced, as little went right in Miami. In mid-May, Hanley Ramírez was suspended for a game by manager Fredi González for not hustling towards a fly ball which cost the team runs and a loss. Nearly two weeks later, Roy Halladay threw a perfect game against Florida, which was the first one thrown against the Marlins in franchise history.

On June 23, with the team sitting at 34–36 along with having a shaky bullpen and inconsistent situational hitting and bench, Loria decided to fire Fredi González along with bench coach Carlos Tosca and hitting coach Jim Presley on June 23. At the time of his dismissal, González's record for the season was 32–34. Edwin Rodriguez was promoted from Triple-A New Orleans as Florida's new manager. Sandwiched between those two announcements were talks with former Rangers and Mets manager Bobby Valentine but those talks broke down. Edwin Rodriguez's first game was a June 23 win against the Baltimore Orioles.

Other disappointments came in the way of injuries to core players, Chris Coghlan, the 2009 NL Rookie of the Year, tore the meniscus in his left knee while jamming a shaving-cream pie in Wes Helms' face. Ricky Nolasco tore the meniscus in his right knee when he took off a shoe. When all was said and done, a club-record 57 players rotated through the clubhouse.

At the All-Star Break, Hanley Ramírez participated in the State Farm Home Run Derby and became the first Marlin to reach the finals. Ramirez lost to David Ortiz but set a Marlins record for most home runs hit in the Derby with 26.

After the All-Star Break, the Marlins went on a surge, getting off to an 11–5 start thanks in large part to Dan Uggla, who also set a Marlins franchise record for total home runs at 144, passing Mike Lowell. In that same week (July 19–July 25), the Marlins had four walk-off base hits, two by Donnie Murphy and one each from Ronny Paulino and Wes Helms. It was that week which brought up the need to be buyers at the trade deadline. Considered in contention for the playoffs, the Marlins traded Rick VandenHurk to the Baltimore Orioles for lefty Will Ohman to shore up a shaky bullpen.

The second half also saw the emergence of rookie outfielders Michael Stanton and Logan Morrison, who replaced the injured Chris Coghlan. Rookie first baseman Gaby Sánchez also put up good numbers, at the top of most lists in home runs, RBIs, and batting average, to contend for the NL Rookie of the Year award.

The Marlins 2010 season was considered a disappointment, as they finished under .500 for the first time since 2007.