The Lake Tanganyika cichlid genus Tropheus Boulenger 1898 consists of stenotypic rock dwellers and contains over a hundred colour morphs. This makes Tropheus an important model for evolutionary research. Yet, the genus taxonomy is confusing and many populations cannot be assigned to a valid species. Notwithstanding its high chromatic and genetic differentiation, the genus was reported to have remained in morphological stasis. A study of an early-diverged species: T. duboisi Marlier 1959, revealed significant intra-population differentiation and refuted the hypothesis of morphological stasis. Different morphological characters, however, showed alternative patterns. Therefore, a verification of which characters are most suitable for species delineation in Tropheus was needed. Lake Tanganyika consists of three subbasins that once formed isolated paleolakes, containing unique cichlid communities. This justified the separate study of the Tropheus species from the central and the southern subbasins. In the central basin, most localities habour two or more sympatric Tropheus species. Surprisingly, heterospecific populations from the same shore were more alike in body proportions than conspecifics from opposite shores. Meristic characters did, however, unite conspecifics, regardless of their origin. As periodic changes in water level drastically changed the shoreline of the shallow parts of the lake, shallow shores harbour younger Tropheus populations than steeper shores. By comparing old and young populations from the southern subbasin, we found that meristics appeared more evolutionary stable than measurements. Hence, both case studies show that meristics are more suitable for species delineation than measurements. Using meristics, seven species were recognised. In the northern and the central subbasin, species could be readily identified. In the south, however, populations could only be assigned to a species by analysing average morphometric values. The relatively low species diversity in Tropheus, compared to its chromatic differentiation, is remarkable. Yet, it is comparable with the situation of other Lake Tanganyika cichlids.