The area near the subpolar front of the East Sea has high primary productivity during the spring season. We conducted two surveys, one in early spring and another in late spring, to assess environmental factors that influence phytoplankton community structure during these times. During early spring, vertical mixing supplied abundant nutrients to the surface. Due to the well-mixed water column, there were high nutrient levels, but total phytoplankton abundances and diversity were relatively low and were dominated by the diatom Chaetoceros spp. During late spring, the water column gradually stratified, with relatively high levels of nutrients in the surface layers near the coastal areas. Phytoplankton abundance and diversity at that time were higher, and there were diatoms (Pseudo-nitzschia spp. and Chaetoceros spp.), cryptophytes, and small flagellates. Pseudo-nitzschia spp. were especially abundant in re-sampled areas. The presence of a stratified and stable water mass and sufficient nitrate led to high phytoplankton growth, even in the open sea during late spring. These findings provide a better understanding of how phytoplankton population dynamics in the East Sea depend on water column stability during both early and late spring seasons.