Long-term monitoring data from two lakes located at different latitudes were used to test the hypothesis that phytoplankton communities respond differently to environmental changes (e.g., global warming and anthropogenic activities, mainly eutrophication). Lake Pyhäjärvi (temperate area) and Lake Taihu (subtropical area) are both shallow and productive lakes. Presence/absence data indicated that phytoplankton taxa present did not change significantly in the two lakes over the last two decades. However, biomass data showed that dominance relationships of species changed in both lakes. Results of assemblage ordination indicated that climate change played a vital role in mediating phytoplankton assemblage dynamics in Lake Pyhäjärvi, while eutrophication was the primary factor driving the phytoplankton assemblage dynamics in Lake Taihu. In Lake Pyäajärvi, the variability of the climatic variables was greater than in Lake Taihu. In Lake Pyhäjärvi, increasing wind speed decreased Secchi depth, promoting shade-tolerant taxa such as Planktothrix. At the same time, increased mixing reduced the loss rate of the heavy taxa such as Tabellaria. Increased nutrient concentrations and water temperature would also promote both Planktothrix and Tabellaria. In the warmer Lake Taihu, the biomass of the dominant Microcystis, which has high optimum temperature for growth, was strongly related to conductivity and less to temperature. Our results showed that climate change potentially enhanced cyanobacteria dominance in lakes Pyhäjärvi and Taihu but by different mechanisms. In Lake Pyhäjärvi, the former dominant species were replaced by cyanobacteria; in Lake Taihu, cyanobacterial dominance was accentuated by climate warming.