This paper describes the species composition, vertical distribution, and the seasonal changes in the biomass of subtidal macrophytes in Sobol Bay (Peter the Great Bay, Sea of Japan). The samples were collected in the depth-range from 0.5 to 4 m. A total of 65 macrophyte species were identified, among which were 10 species of Chlorophyta, 17 of Phaeophyceae, 37 of Rhodophyta and 1 of Magnoliophyta. Multivariate analyses were performed to detect spatial and temporal variations. Maximum species richness was registered in June, with a particularly dramatic biomass increase of brown algae. Both the number of species and the biomass of macrophytes decreased with increasing depth. Depth clearly affected the patterns of seasonal fluctuations of the species composition and biomass. In the study area, the species composition of the shallow-water algal assemblages was more stable throughout the year compared to that of the algal assemblages found in deeper waters. In total, four macrophyte assemblages were identified in the bay. A Phyllospadix iwatensis and Coccophora langsdorfii dominated assemblage occupied muddy-gravel bottoms in depths from 0.5 to 2 m throughout the year. An assemblage, co-dominated by annual brown algae Desmarestia viridis and Costaria costata, occurred at depths more than 3 m at late spring. Two other assemblages occurred on the rock and boulder bottom at 0.5–2 m depths, but they were temporally separated. An assemblage co-dominated by annual laminarian algae (Undaria pinnatifida and Costaria costata) developed at late spring and was succeeded in the autumn and winter by a Tichocarpus crinitus, Ulva lactuca, Sargassum pallidum and Codium fragile co-dominated assemblage. A comparison between the data obtained in the present study and the results of a previous study conducted in 1927 shows that the macrophytes assemblages in Sobol Bay underwent little change.