Decapod assemblages in Zostera marina beds from two bays adjacent to unvegetated habitats were investigated to assess their influence on decapod assemblages. Thirty-eight decapod species belonging to 4 taxa were collected using a small beam trawl at four habitat types from two different locations off the coast of Namhae Island, southern Korea. Dominant decapod taxon at all habitats was the caridean shrimps, with Eualus leptognathus, Heptacarpus pandaloides, Latreutes anoplonyx, La. laminirostris and Palaemon macrodactylus being the most abundant caridean species. Crabs were characterized by the highest biomass, but moderate species richness and abundance. Penaeoids and sergestoids shrimps only accounted for <1% of the total decapod abundance. The number of species, their abundance, and the diversity of decapod assemblages varied greatly by habitat type, season, and diel patterns. Species number and abundance peaked in seagrass beds of southern exposed bays during the autumn, and were lowest in unvegetated habitats during the summer months. Diel decapod species and catch rates were higher at night. Dense seagrass vegetation and nighttime supported greater decapod species richness and higher mean densities, but not diversity. Multivariate analyses revealed that habitat type and season significantly affected the structure of decapod assemblages, but diel patterns had a minor influence. Among decapod species, Pa. macrodactylus and Pugettia quadridens characterized the decapod assemblages in seagrass beds at the northern semi-closed bay, while Telmessus acutidens, Crangon affinis, Cr. hakodatei, Charybdis japonica and Portunus sanguinolentus were significantly associated with both vegetated and unvegetated habitats at the southern exposed bay, with the former two species more abundant during winter and spring.