Cypriniforms, commonly known as carps, suckers, minnows, and loaches, comprise the largest order of freshwater fishes and can be found throughout North America, Eurasia, and Africa. This group exhibits great diversity in body size and form and the skeletal variation has been well documented in the literature. In particular, morphological variations in the gill arch skeleton have been used extensively in phylogenetic studies to elucidate the relationships among the six families. Nearly all morphological studies have a skeletal focus due to the greater difficulties of collecting muscle data, i.e., greater number of specimens needed, destructive dissections, and increase in time commitment. Consequently, the scope of phylogenetic variation in the associated musculature among the families remains largely unknown. One family, the Cyprinidae, has been well documented and generalizations from cyprinid descriptions have been applied to the other cypriniform families. The purpose of this study has been to address whether these generalizations are accurate. Additionally, using the descriptions for cyprinid gill arch musculature, this study proposed a set of testable predictions concerning the relationships between gill arch skeletal variation and the associated musculature in three of the six families (Botiidae, Catostomidae, and Cyprinidae). The results from this study demonstrate there is not a simple relationship between skeletal and muscle variation. There was a great reduction in the number of gill arch muscles present in the catostomid and the botiid compared to the cyprinids. Furthermore, the catostomid and the botiid also showed a reduction in the size of other gill arch muscles compared to the cyprinids, indicating that generalizations from cyprinid descriptions are inaccurate. This great variation in the number and size of muscles likely arose in response to the adaptations required for differences in food processing among these fishes.