Here we present the first study comparing all the paired appendages muscles of representatives of each major extant gnathostome group. We address a crucial and enigmatic question in evolutionary and comparative anatomy: Why are the pelvic and pectoral appendages of gnathostomes, and particularly of tetrapods, in general so similar to each other? We argue that an integrative analysis of the new myological data and the information from the literature contradicts the idea that the forelimbs and hindlimbs are serial homologues. The data show that many of the strikingly similar fore- and hindlimb muscles of extant tetrapods evolved independently in each appendage because the ancestors of extant gnathostomes and osteichthyans only had an adductor and an abductor in each fin. Therefore, these data contradict the idea that at least some muscles present in the tetrapod fore- and hindlimbs were already present in some form in the first fishes with pectoral and pelvic appendages, as the result of an ancestral duplication of the paired appendages leading to a true serial homology. The origin of the pectoral girdle was instead likely related to head evolution, as illustrated by the cucullaris of gnathostomes such as chondrichthyans inserting onto both the branchial arches and pectoral girdle. Only later in evolution the cucullaris became differentiated into the levatores arcuum branchialium and protractor pectoralis, which gave rise to the amniote neck muscles trapezius and sternocleidomastoideus. These changes therefore contributed to an evolutionary trend towards a greater anatomical and functional independence of the pectoral girdle from head movements.