The genotype of an organism is its complete set of genetic material.[1] However, the term is often used to refer to a single gene or set of genes, such as the genotype for eye color. The genes partly determine the observable characteristics of an organism (its phenotype), such as hair color, height, etc.[2] An example of a characteristic determined by a genotype is the petal color in a pea plant. The collection of all genetic possibilities for a single trait are called alleles; two alleles for petal color are purple and white.[3]

Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal colour in a pea plant. The letters B and b represent alleles for colour and the pictures show the resultant flowers. The diagram shows the cross between two heterozygous parents where B represents the dominant allele (purple) and b represents the recessive allele (white).

The genotype is one of three factors that determine phenotype. The other two are the environmental (not inherited) and the epigenetic (inherited) factors. Not all individuals with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype. One would typically refer to an individual's genotype with regard to a particular gene of interest and the combination of alleles the individual carries (see homozygous, heterozygous).[4] Genotypes are often denoted with letters, for example Bb, where B stands for one allele and b for another.

Somatic mutations that are acquired rather than inherited, such as those in cancers, are not part of the individual's genotype. Hence, scientists and physicians sometimes refer to the genotype of a particular cancer, that is, of the disease as distinct from the diseased.

The term genotype was coined by the Danish botanist Wilhelm Johannsen in 1903.[5]