Vertebrate craniofacial development is a highly dynamic process with many of the mechanisms regulating more subtle variations in morphology poorly understood. Cichlid fishes exhibit a diverse array of craniofacial morphologies well suited to study these more subtle variations. A conserved feature of vertebrate craniofacial development is the formation of embryonic pharyngeal pouches, which are the basis of serially homologous bones (i.e., the pharyngeal skeleton). Of these structures the bones that make up the gill arch skeleton, primarily the epibranchial (EB) dorsally and ceratobranchial (CB) ventrally, have received little attention in the context of development and evolution despite the multifaceted demands of the arch in respiration and feeding. Here, we sought to characterize morphological variation of the cichlid gill arch, assess the degree to which it is associated with foraging ecological, and uncover its genetic basis. Our quantification of gill arch shape was twofold with a 3D geometric morphometric analysis of CB1 and a ratio of CB1 to EB1 length as a proxy of arch curvature. These methods were employed in two main populations: a natural population consisting of 85 species of cichlid and a F5 hybrid population consisting of 402 hybrids, derived from crossing two species with divergent pharyngeal skeletal shape, Labeotropheus fuelleborni (LF) and Tropheops sp. “red cheek” (TRC). Our findings suggest that gill arch curvature exhibits market variation among species and differs between species with different foraging modes. In the hybrid population we saw a recapitulation of the variations in shape observed between species. Next, we used quantitative trait locus (QTL) analysis to identify 5 regions of the genome associated with gill arch shape. Modes of inheritance ranged from additive to dominant to overdominant, suggesting a complex genetic basis. Of those 5 regions, the QTL on chromosome 6 provided as a candidate for fine mapping to increase our genotypic-phenotypic resolution within that interval. Through fine mapping we were able to identify a total of 7 candidate genes that may be responsible for regulating CB1 shape, including fgf20a, a known bone remodeler. Overall, our findings suggest that the ecological consequences of and genetic basis for gill arch shape is worthy of further study.