The taxonomic status of the zooplanktivorous cichlidsCopadichromis mlotoandC. virginalishas been confused since their original descriptions by lles in 1960. Whilst two forms ofC. virginalis, ‘Kaduna’ and ‘Kajose’, were distinguished in the type material,C. mlotohas not been positively identified since its original description. Here we re-examined the types as well as 54 recently collected specimens from multiple sampling locations. Genome sequencing of 51 recent specimens revealed two closely related but reciprocally monophyletic clades. Geometric morphological analysis indicated that one clade morphologically encompasses the type specimens ofC. virginalisidentified by Iles as the Kaduna form, including the holotype, whilst the other clade encompasses not only the paratypes identified as the Kajose form, but also the type series ofC. mloto. Given that all three forms in Iles’s type series are from the same locality, that there are no meristic or character states to differentiate them and that there are no records of adult maleC. mlotoin breeding colours, we conclude that the Kajose form previously identified asC. virginalisrepresents relatively deeper bodied sexually active or maturing individuals ofC. mloto.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10750-022-05025-1.