Mesoscale processes such as eddies and fronts are ubiquitous in the open ocean and strongly influence nutrient supply and phytoplankton distribution. However, conventional sampling often misses rapid biological responses to these dynamic features. During a cruise in the Kuroshio‑Oyashio Extension of the NW Pacific, we conducted high-resolution surface sampling of phytoplankton communities using automated flow cytometry, along with concurrent temperature and salinity measurements. We focused on a transect crossing the Kuroshio axis and extending into the Oyashio region, covering an anticyclonic warm-core eddy (AWE), a frontal zone, and two cold-core eddies (transient and stable). Among the 11 groups identified by flow cytometry, picophytoplankton dominated the community. Total abundance was lowest in the AWE, which conversely had the highest diversity and a distinct community composition. SIMPER analysis further revealed distinct habitat preferences among picophytoplankton, with Synechococcus exclusively in the AWE and Prochlorococcus only in surrounding waters. Notably, the frontal zone acted as both a barrier and enrichment site, with elevated abundance and transitional communities. The transient cold-core eddy, sampled during its formation, showed higher abundance and diversity than the stable one, likely due to higher nutrient input. RDA analysis showed that temperature and salinity together explained ~73% of community variation, underscoring the role of mesoscale processes in shaping phytoplankton distribution and reinforcing the importance of fine-scale physical-biological coupling in this dynamic region.