The morphological diversity of Malawi and Tanganyika cichlids has often been qualitatively described, but rarely have hypotheses based on these descriptions been tested empirically. Using landmark based geometric morphometrics, shapes are analyzed independent of other aspects of the body form (e.g., size). The estimation of shape disparity, the quantitative measure of the variance of these raw shapes, can then be applied in order to objectively test hypotheses about morphological diversity. The shape disparity within and between different groups is explored as well as how it is partitioned within the cichlid body. Tanganyika cichlids are found to have significantly greater shape disparity than Malawi cichlids. Ectodini is found to have significantly greater shape disparity than other Great Lake tribes. Piscivorous cichlids are significantly more disparate in shape than cichlids with other diets, and the shape disparity of the cranial region was significantly greater than that of the post-cranial region.