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The shifts among bloom-forming cyanobacteria have attracted increasing attention due to the reductions in nitrogen and phosphorus during the eutrophication mitigation process. However, knowledge is limited regarding the pattern and drivers of the shifts among these cyanobacterial genera. In this study, we performed a 7-year long, monthly investigation in Lake Chaohu, to analyze the interannual and seasonal shifts between <i>Microcystis</i> and <i>Dolichospermum</i>. Our results showed that <i>Microcystis</i> was the dominant cyanobacterium in the western lake region in summer, whereas <i>Dolichospermum</i> was dominant in the other regions and seasons. The <i>Microcystis</i> biomass and ratio were driven primarily by total phosphorus and temperature. The sensitivity of <i>Dolichospermum</i> to nutrients and temperature was relatively weak compared to that of <i>Microcystis</i>. The shifts between <i>Microcystis</i> and <i>Dolichospermum</i> might be led by <i>Microcystis</i>. If the temperature and phosphorus level were relatively high, then <i>Microcystis</i> grew rapidly, and competitively excluded <i>Dolichospermum</i>. If the nutrient level, especially the phosphorus level, was low, then the exclusive power of <i>Microcystis</i> was weak, and <i>Dolichospermum</i> maintained its dominance, even in summer. The key temperature (~17 °C) determined the dominance of the two cyanobacteria. <i>Microcystis</i> never dominated, while <i>Dolichospermum</i> was always dominant below the key temperature. <i>Microcystis</i> and <i>Dolichospermum</i> had different means of responding to the interaction of temperature, nitrogen and phosphorus. The <i>Dolichospermum</i> biomass was sensitive to the variation in nitrogen level, and the sensitivity depended on temperature. While the <i>Microcystis</i> biomass was sensitive to the variation in phosphorus level, and the sensitivity depended on temperature and total nitrogen. The different ways might contribute to the succession of the two cyanobacteria. Our findings will be helpful for improving the understanding of the shift process between <i>Microcystis</i> and <i>Dolichospermum</i>.