The endemic Lake Tanganyika cichlid genus Tropheus Boulenger 1898 consists of highly stenotypic rock dwellers, whose limited capacity for dispersal gave rise to over a hundred colour morphs. This made Tropheus an important model for evolutionary research. Yet, the genus taxonomy is confusing with most species being ill-defined and with many populations that cannot be unambiguously assigned to a valid species. As such, a revision of the genus is needed. Notwithstanding its high chromatic and genetic differentiation, the general morphology of Tropheus was, until recently, reported to have remained static. This hypothesis of morphological stasis was investigated in Tropheus duboisi Marlier 1959, an early diverged Tropheus that displays only minor intra-specific differences in colour pattern and is less stenotypic than its congeners. The results, however, revealed significant morphological differentiation between geographically isolated populations. This indicates that problems for a morphological revision of the genus not only result from the low degree of morphological differentiation between species, but also from the presence of intra-specific differentiation. One of the long-standing problems in Tropheus is the similarity between T. annectens Boulenger 1900 and T. polli Axelrod 1977, which are sometimes regarded as synonyms. Using museum specimens and recently collected material and a multidisciplinary approach, this problem could be resolved. Surprisingly, the morphological differences found between different populations of these two highly resembling species are mirrored by the differences encountered between populations of another, sympatric, Tropheus species. This finding suggests a strong environmental effect on morphology.