Color morphism occurs in the species. A near-black melanistic form occurs regularly. Jaguars with melanism appear entirely black, although their spots are still visible on close examination.

The black morph is less common than the spotted form but, at about six percent of the population, it is several orders of magnitude above the rate of mutation. Hence, it is being supported by selection. Some evidence indicates the melanism allele is dominant. The black form may be an example of heterozygote advantage ; breeding in captivity is not yet conclusive on this.

Melanistic jaguars are informally known as black panthers but (as with all forms of polymorphism) they do not form a separate species.