An example is the gene for blossom color in many species of flower — a single gene controls the color of the petals, but there may be several different versions (or alleles) of the gene. One version might result in red petals, while another might result in white petals. The resulting color of an individual flower will depend on which two alleles it possesses for the gene and how the two interact.

An allele is an alternative form of a gene (in diploids, one member of a pair) that is located at a specific position on a specific chromosome.

Diploid organisms, for example, humans, have paired homologous chromosomes in their somatic cells, and these contain two copies of each gene. An organism in which the two copies of the gene are identical — that is, have the same allele — is called homozygous for that gene. An organism which has two different alleles of the gene is called heterozygous. Phenotypes (the expressed characteristics) associated with a certain allele can sometimes be dominant or recessive, but often they are neither. A dominant phenotype will be expressed when at least one allele of its associated type is present, whereas a recessive phenotype will only be expressed when both alleles are of its associated type.

However, there are exceptions to the way heterozygotes express themselves in the phenotype. One exception is incomplete dominance (sometimes called blending inheritance) when alleles blend their traits in the phenotype. An example of this would be seen if, when crossing Antirrhinums — flowers with incompletely dominant "red" and "white" alleles for petal color — the resulting offspring had pink petals. Another exception is co-dominance, where both alleles are active and both traits are expressed at the same time; for example, both red and white petals in the same bloom or red and white flowers on the same plant. Codominance is also apparent in human blood types. A person with one "A" blood type allele and one "B" blood type allele would have a blood type of "AB".

A wild type allele is an allele which is considered to be "normal" for the organism in question, as opposed to a mutant allele which is usually a relatively new modification.

(Note that with the advent of neutral genetic markers, the term 'allele' is now often used to refer to DNA sequence variants in non-functional, or junk DNA. For example, allele frequency tables are often presented for genetic markers, such as the DYS markers.) Also there are many different types of alleles.