Telmatochromis temporalis is a cichlid fish endemic to Lake Tanganyika. Two morphs of this species, normal and dwarf, form a good model for the study of ecological speciation through divergent natural selection on body size. This study reports a third morph of this species, slender morph, which was collected from deep waters off Kasenga, Zambia, whereas the normal morph inhabits shallow waters of the same locality. This study examined morphological characters and mitochondrial DNA sequences in 18 populations of the three T. temporalis morphs and two closely related species. The slender morph was morphologically similar to the normal and dwarf morphs of the same species, but clearly differed from closely related species. Genetic analyses showed that the slender morph was closest to but significantly different from the parapatric normal morph, suggesting reproductive isolation between them. Due to the lack of colour differences between morphs and of obvious geographical barriers between habitats, reproductive isolation between these morphs may be attributed to ecological factors, rather than sexual or geographical segregation. Further studies examining the evolution of the slender morph may deepen our knowledge of initial stages of speciation, like in the dwarf morph.