Shape variation in trophic morphology between species in two trophic guilds (zooplankton and epilithic algal feeders) was investigated using landmark-based geometric morphometrics. Three disarticulated bone elements from the head region were examined; the neurocranium, the premaxilla and lower jaw. From separate analyses of each bone element, significant shape variation was identified between species in each trophic guild. The deformation grids generated revealed that, for the zooplankton feeders, Ctenopharynx pictus has a longer neurocranium, a longer and ventrally directed vomer, a larger orbit, a shorter ascending arm, a shorter maxillad spine, and a more compressed articular bone relative to Copadichromis borleyi. In algal feeders, Labeotropheus fuelleborni has a shorter neurocranium, a smaller orbit, a ventrally directed vomer, a longer ascending arm, a shorter dentigerous arm, increased height of the articular process, and a more elongated dentary than Petrotilapia genalutea. Observed anatomical differences are discussed in terms of function, specifically with respect to the feeding microhabitat differentiation between species in each trophic guild. These differences enable us to appreciate the role that trophic morphology plays in enhancing ecological segregation, leading to coexistence of the species.