Seagrass habitats are highly productive areas that support vegetative habitats and provide shelter for various marine animals. In seagrass beds, vegetation patterns are important factors that control faunal assemblage structure. In this study, we surveyed fish assemblage structures in Zostera marina beds and in adjacent unvegetated habitats to assess the influences of seagrass vegetation and biomass on fish assemblage structures. In total, fifty-four fish species belonging to 30 families were collected using a small beam trawl at both seagrass beds and unvegetated habitats from two different areas off the coast of Namhae Island, South Korea. The dominant fish species in seagrass beds were Sebastes inermis and Rudarius ercodes, whereas Acanthogobius flavimanus and Takifugu niphobles were the most abundant fish species in unvegetated habitats. The number of species, their abundance, and the diversity of fish assemblages varied greatly by habitat type, study site, and season. Abundance peaked in seagrass beds and during the spring, and were lowest catch rate in unvegetated habitats and during the winter months. Multivariate analyses revealed that habitat type, site, and season affected the structure of fish assemblages. Seagrass vegetation supported higher densities and greater fish species richness, but not species diversity. Among the dominant species, Lateolabrax japonicus, Sebastes schlegelii, Syngnathus schlegeli, and Rudarius ercodes characterized the fish assemblages in seagrass beds, with the former two more abundant under conditions of higher seagrass biomass. Gobiid species were significantly correlated with unvegetated habitats.