Phytoplankton productivity and community structure in marginal seas have been altered significantly during the past three decades, but it is still a challenge to distinguish the forcing mechanisms between climate change and anthropogenic activities. High time-resolution biomarker records of two 210Pb-dated sediment cores(#34: 28.5°N, 122.272°E; CJ12-1269: 28.861 9°N, 122.515 3°E) from the Min-Zhe coastal mud area were compared to reveal changes of phytoplankton productivity and community structure over the past 100 years. Phytoplankton productivity started to increase gradually from the 1970 s and increased rapidly after the late 1990 s at Site #34; and it started to increase gradually from the middle 1960 s and increased rapidly after the late 1980 s at Site CJ12-1269. Productivity of Core CJ12-1269 was higher than that of Core #34. Phytoplankton community structure variations displayed opposite patterns in the two cores. The decreasing D/B(dinosterol/brassicasterol) ratio of Core #34 since the 1960 s revealed increased diatom contribution to total productivity. In contrast, the increasing D/B ratio of Core CJ12-1269 since the 1950 s indicated increased dinoflagellate contribution to total productivity. Both the productivity increase and the increased dinoflagellate contribution in Core CJ12-1269 since the 1950–1960s were mainly caused by anthropogenic activities, as the location was closer to the Changjiang River Estuary with higher nutrient concentration and decreasing Si/N ratios. However, increased diatom contribution in Core #34 is proposed to be caused by increased coastal upwelling, with higher nutrient concentration and higher Si/N ratios. Phytoplankton productivity and community structure in marginal seas have been altered greatly during the past three decades, but it is still a challenge to distinguish the forcing mechanisms between climate change and anthropogenic activities. High time-resolution biomarker records of two 210Pb-dated sediment cores # 34: 28.5 ° N, 122.272 ° E; CJ12-1269: 28.861 9 ° N, 122.515 3 ° E) from the Min-Zhe coastal mud area were compared to reveal changes of phytoplankton productivity and community structure over the past 100 years. Phytoplankton productivity started to increase gradually from the 1970 s and increased rapidly after the late 1990 s at Site # 34; and it started to increase gradually from the middle 1960 s and increased rapidly after the late 1980 s at Site CJ12-1269. Core CJ 12-1269 was higher than that of Core # 34. Phytoplankton community structure variations displayed opposite patterns in the two cores. The decreasing D / B (dinosterol / brassicasterol) ratio of Core # 34 since the 1960 s revealed increased diatom contribution to total productivity. The contrast D / B ratio of Core CJ12-1269 since the 1950 s indicated increased dinoflagellate contribution to total productivity. Both the productivity increase and the increased dinoflagellate contribution in Core CJ 12-1269 since the 1950-1960s were mainly caused by anthropogenic activities, as the location was closer to the Changjiang River Estuary with higher nutrient concentration and decreasing Si / N ratios. However, increased diatom contribution in Core # 34 is proposed to be caused by increased coastal upwelling, with higher nutrient concentration and higher Si / N ratios.