Owing to its high degree of complexity and plasticity, the cichlid pharyngeal jaw apparatus has often been described as a key evolutionary innovation. The majority of studies investigating pharyngeal muscle behavior and function have done so in the context of feeding. Analysis of enzyme activities (citrate synthase, 3-hydroxyacyl-CoA dehydrogenase and L-lactate dehydrogenase) of pharyngeal muscles in the Lake Malawi cichlid Tramitichromis intermedius revealed differences between pharyngeal jaw muscles and between males and females. Therefore, these muscles have different performance characteristics, resulting in different functional characteristics of the muscles within the complex. Furthermore, the differences between muscles of males and females represent fundamental differences in muscular metabolic processes between sexes. This study is the first to demonstrate that the pharyngeal anatomy is not only used for food processing but is possibly responsible for sound production, in turn influencing sexual selection in cichlid fish.