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Intra-specific morphological variation in the cichlid Tropheus duboisi from 10 localities over its entire known distribution area along the central eastern and northern shore of Lake Tanganyika was investigated. This revealed significant differences between various populations that are geographically isolated. These morphological observations only partially correspond to the results of a haplotype network, based on mtDNA. In addition, a difference in the timing of the onset of the adult colour pattern was discovered for one isolated population. The occurrence of morphological intra-specific differentiation is discussed with respect to the basal position of T. duboisi within Tropheus as well as to the presumed morphological stasis of the genus. [ABSTRACT FROM AUTHOR]