Muscle morphology in the Placodermi can be inferred by comparison to extant gnathostomes (Chondrichthyes (Actinopterygii Sarcopterygii)). Examination of the chondrichthyan hypobranchial musculature suggested a comparable musculature for placoderms, including the coracomandibularis and coracohyoideus, acting separately to depress the mandible and hyoid arch. In sharks, this was associated with the absence of a mandibulohyoid ligament functioning in mandible depression, a characteristic feature of actinopterygians and sarcopterygians. Additionally, the coracobranchiales muscles depress the chondrichthyan ventral gill arches, the clavobranchiales being the corresponding muscles in actinopterygians and sarcopterygians. These muscles and ligaments are not preserved in placoderms, but their attachments can be compared to those of extant gnathostomes. On the placoderm lower jaw, attachment surfaces for the mandibulohyoid ligament are only present in derived taxa and position relative to the jaw joint suggests the ligament functioned poorly (or not at all). This compares to the chondrichthyan condition, but attachment surfaces on the placoderm trunkshield indicate that while some primitive placoderms possessed a coracobranchialis musculature, other derived taxa possessed a clavobranchialis.

The Osteostraci are the most closely related agnathans to the jawed vertebrates, and lack muscles involved in active inspiration, the evolution of which was linked to increased activity near the origin of jawed vertebrates. Since overall morphology suggests osteostracans were active animals, absence of these muscles may instead relate to the absence of segmented gill arches and the anterior position of the osteostracan pectoral fin. The latter may affect development of the hypobranchial musculature, questioning homology of these muscles in lampreys and jawed vertebrates.