Organisms sampled for population level research are typically assigned to species by morphological criteria. But if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock-dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified by investigators using adult male coloration patterns. Given high local endemism of male color patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped, and separately assigned: (1) to morphospecies using photographs; and (2) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (1) adult male-limited sampling and (2) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well-demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.