The genus Apistogramma is among the most speciose of South American cichlid genera with around 70 species valid at present but many more awaiting description. In addition many species exist in two or more geographical colour forms which may or may not turn out to be distinct in the future. Hobbyists tend to label these with collection data if available in order to avoid mixing them and the potential of hybridisation.

Member species have also been organised into a series of species lineages, sublineages, complexes and groups by authors in order to better separate them.