Imprecise usage of terminology can lead to confusion when trying to compare cranial musculature between taxa from different higher-order groups. The present study aimed to present hypotheses of muscle homology between taxa from four modern gnathostome groups: Actinopterygii (Amia calva), Sarcopterygii (Latimeria chalumnae), Elasmobranchii (Squalus acanthias, Chlamydoselachus anguineus), and Holocephali (Hydrolagus colliei). Muscle homologies are hypothesized based on topological data taken from the anatomical literature and supplemented by new observations of Hydrolagus colliei. Hypothesized muscle groups are tested for congruence against accepted gnathostome phylogeny. From these data, eight muscle groups are identified that are unambiguously homologous across all taxa examined. Four more muscle groups are found to be homologous across a majority of the taxa. Twelve muscle groups are hypothesized to be basal across all gnathostomes. A muscle in Hydrolagus previously called both a geniohyoideus and interhyoideus is here renamed ‘mandibulohyoideus’ to reflect its apomorphic condition. The presence of coracomandibular muscles in all groups supports the hypothesis that basal jaw depression systems in gnathostomes were not linked to hyoid movement, but independently operated by this muscle. The study also offers new insight into muscle reconstruction in fossil groups (Placodermi). © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 195–216.