The craniofacial skeleton is one of the most sexually dimorphic traits in humans, showing shape differences in structures such as the jaw. The molecular mechanisms that facilitate this variation between males and females, and when in development these differences arise, are unknown. To determine the pattern of craniofacial sexual dimorphism, we conducted geometric morphometric shape analysis on craniofacial structures in five species of Lake Malawi cichlids. These fish have undergone an adaptive radiation resulting in closely-related species presenting a spectrum of craniofacial morphologies based on different trophic strategies (biting versus suction-feeding), making them ideal models for studying species- and sex-specific craniofacial variation. Although there were larger effects of species and age, we found that sex is a significant contributor to bone shape. For example, p=1.1e-12 for species, p=7.8e-6 for age, and p=0.04 for sex on analysis of the lateral mandible. Notably, differences in overall lateral and ventral craniofacial shape between males and females differed between species. Together, these suggest that both sex, and interactions between species-specific genetics and sex, are contributing to the incredible craniofacial diversity present in these species. We found that manipulation of estrogen and progesterone hormone signaling during early bone patterning has a significant effect on craniofacial shape. This suggests a possible molecular mechanism that underlies sex dimorphism, and highlights the importance of hormone signaling in bone development before puberty. Altogether, we find that sexual dimorphism significantly contributes to phenotypic variation in the face, has distinct patterns in animals with alternate feeding strategies, and may occur through variation in hormone signaling.