The evolution of jaws in cichlid fishes of the East African Great Lakes is a textbook example of adaptive radiation in vertebrates. Karl Liem postulated that this adaptive radiation has been possible due to the functional decoupling of two cichlid functional units – the pharyngeal jaw (PJ) and the oral jaw (OJ). This functional decoupling of the jaws has enabled the OJ to be relieved of its dual role of prey capturing and processing and has allowed the PJ to take on the role of prey processing. As a result, African cichlids have adapted the morphology of their functional units (i.e., oral jaws) to specialize in a feeding mechanism best suited for their habitat. However, global morphological changes (across the OJ and PJ) are understudied, especially, at the genetic level. In this study, two rock dwelling species of African Cichlids from Lake Malawi were used - Labeotropheus fuelleborni (LF) and Tropheops “red cheek” (TRC). Both species have distinct craniofacial morphologies for specialized benthic feeding (LF) and for generalized feeding (TRC). This morphological variation allowed us to investigate the functional decoupling of the jaws by studying differences in bone shape and muscle volumes in an F5 hybrid population. Strong phenotypic correlations were observed between and within the tissues of the OJ and PJ. Further, to identify phenotype to genotype associations, a Quantitative Locus (QTL) analysis and a fine mapping analysis was conducted. The results show some evidence of overlapping genetic control (i.e., pleiotropy) suggesting some genetic coupling between the two jaws.