Short-term tidal and diel variations of autumn fish assemblage in a Zostera marina bed were investigated using 3 h interval samplings for 24 h in both spring and neap tide using a small beam trawl. A total of 1,346 fishes belonging to 19 species were collected at spring tide, whereas 1,115 fishes belonging to 17 species were at neap tide. The common fish species were Nuchequula nuchalis, Acanthogobius flavimanus, Takifugu niphobles, Acentrogobius pflaumii, and Pholis nebulosa with the former three species dominating at spring tide, while the latter two species being abundant at neap tide. Diel variation in abundance was significant with higher abundance at night than day, but there were no significant differences between spring and neap tides, and between ebb and flood tides (three-way ANOVAs). Diel variation in the abundance of fishes may be influenced by tidal range and cycle, and day-night differences of food availability and behaviors of fishes indirectly. Non-metric multidimensional scaling (nMDS) ordination and analysis of similarity (ANOSIM) results revealed significant differences in species compositions both between day and night, and between spring and neap tide. Eelgrass beds are highly productive marine ecosystem, and thus, our results will contribute to conservation of seagrass ecosystem in the study area.