Naphthoquinones constitute a class of organic compounds structurally related to naphthalene. Two isomers are common for the parent naphthoquinones:

• 1,2-Naphthoquinone
• 1,4-Naphthoquinone

• Alkannin
• Hexahydroxy-1,4-naphthalenedione
• Juglone
• Lapachol
• Lawsone
• Menatetrenone
• 2-Methoxy-1,4-naphthoquinone, a compound found in Impatiens species
• Nigrosporin B
• Phylloquinone
• Plumbagin
• Spinochrome B
• Spinochrome D
• Vitamin K and related compounds
  • Phylloquinone
  • Vitamin K2
  • Menadione (2-Methyl-1,4-naphthoquinone)

• 5,8-Dihydroxy-1,4-naphthoquinone and dihydroxynaphthoquinones
• Atovaquone
• Buparvaquone, an antiprotozoal drug used in veterinary medicine
• Diazonaphthoquinone, a diazo derivative of naphthoquinone
• 1,2-Naphthoquinone, from the biodegradation of naphthalene.

• Hydroxynaphthoquinones