Landmark-based geometric morphometric techniques were used to test the hypothesis that Petrochromis spp. from Lake Tanganyika are ecomorphologically equivalent to Petrotilapia spp. from Lake Malawi. Both genera are epilithic algal feeders and inhabit the rocky shores of their respective lakes. We investigated the morphological component of the ecomorphology hypothesis by investigating body shape, using landmark-based morphometric techniques. A MANOVA revealed significant differences among species and an ordination of all species along the first two CV axes showed clear separation of the two genera in the morphospace with Petrochromis fasciolatus as an intermediate. A thin-plate spline analysis revealed that Petrochromis spp. had a deeper, broader anterior body, larger gape, shorter anal fin base and narrower caudal peduncle than Petrotilapia spp. Basically, differences between lakes were found, but there were no similarities or clusters of presumptive ecomorphs. Based on such results, we reject the hypothesis of morphological equivalence between these two genera. However, considering the non-significant difference in body shape revealed between P. fasciolatus, Petrotilapia genalutea and Petrotilapia ‘mumbo blue’, we conclude that these three species represent morphological equivalence and hence display a best example of convergent evolution.