In Lake Malawi cichlids, comparisons of feeding morphology have typically been performed at the genus level, with little emphasis on interspecific comparisons. Variation in jaw shape can be a powerful predictor of feeding performance and habitat preference. Jaw morphology and habitat partitioning were examined among species in the Lake Malawi rock-dwelling species complex, Tropheops. Although Tropheops species varied in a variety of craniofacial characters, lower jaw shape was the focus of this study because of its close association with feeding performance in bony fishes. Significant differences were observed among five microhabitat variables measured in situ for six Tropheops species at two field sites in southern Lake Malawi in July and August, 2001. Depth was identified as a major axis of trophic niche partitioning, and species-specific differences in lower jaw shape and foraging strategy were correlated with depth distributions among species. These data are consistent with the hypothesis that competition for trophic resources (epilithic organisms) has led to habitat partitioning and the establishment and maintenance of distinct trophic morphologies within the Tropheops species complex. Detailed morphological analyses of inter- (and intra-) specific trophic variation in Lake Malawi cichlids will likely lead to important insights into the proximate mechanisms that underlie cichlid trophic diversity.