Abstract: To compare the phytoplankton community of the Bohai Sea and the Yellow Sea, we collected water samples from 50 stations (31.19 °N－39.82 °N, 118.89 °E－125.65 °E) in the Bohai Sea (BS), North Yellow Sea (NYS) and South Yellow Sea (SYS) in the summer of 2013, and characterized the phytoplankton community structure by studying the species composition, abundance, dominant species and diversity. The results showed that the highest species number and Shannon-Wiener diversity index were detected in SYS, followed by NYS and BS. High diversity index regions were distributed on the south sea area of Shandong Peninsula, the central area of NYS and the adjoining waters of the Yangtze River. Phytoplankton abundance throughout the water column was in the range of 0.01×10³～418.2×10³ cells/L, and the average abundance of the BS, NYS and SYS were (14.6±12.8) ×10³ cells/L, (11.5±14.9) ×10³ cells/L and (35.7±92.3) ×10³ cells/L, respectively. The phytoplankton assemblages were mainly comprised of Dinophyta and Bacillariophyta. Dinophyta accounted for 46.6%, 73.1% and 22.1% of water column phytoplankton abundance and Bacillariophyta accounted for 46.6%, 73.1% and 22.1% in the BS, NYS and SYS, respectively. Phytoplankton of the BS and SYS were mainly distributed in the surface and subsurface layer while that of the NYS were mainly distributed in the middle to bottom layer.