Elucidation of the causes of cyanobacterial harmful algal blooms (CHABs) may be a precondition for their control. We have investigated Lake Chaohu since 2007; identifying phytoplankton species, observing seasonal variation in dominant species, measuring primary productivity, detecting changes in limnological characteristics, identifying "leading factors", and then assaying the ecophysiology of photosynthesis in the dominant cyanobacteria. We also analyzed the historical events relating to CHABs in this lake. Our studies showed that phytoplankton diversity varied seasonally, and dominant cyanobacteria represented more than 74% of the total phytoplankton cells. Dominant species in 2008 to 2009 included Microcystis viridis (in April, May, June, October, November and December); M. wesenbergii (in July and August); M. aeruginosa (in September); and Anabaena flos-aquae (in January, February and March). Blooms were recorded over 100 years ago in this lake, and no appropriate explanations have been advanced for their causes. Since the 1930s, researchers have presented the following ten hypotheses on bloom formation: (A) the TN/TP hypothesis; (B) the inorganic nitrogen hypothesis; (C) the buoyancy hypothesis; (D) the storage strategy hypothesis; (E) the low light hypothesis; (F) the high pH/low CO₂ hypothesis; (G) the elevated water temperature hypothesis; (H) the trace element hypothesis; (I) the zooplankton grazing hypothesis; and (J) the evolutionary adaptation hypothesis. Although these hypotheses explain why cyanobacteria successfully compete over eukaryotic algae in most lakes and reservoirs, they cannot clarify why different dominant cyanobacterial species appear in seasonal succession in Lake Chaohu. A new hypothesis is needed. Based on our understanding, we have constructed "the photosynthesis of dominant species hypothesis", as follows: (1) Blooms include various species of cyanobacteria and algae. Bloom initiation is related to cell density, and also to primary productivity. We collected and measured phytoplankton monthly in different water depths at six points in the western part of Lake Chaohu. In 2008 to 2009, collected phytoplankton consisted of 85 species (in 5 phyla). Both cell density and primary productivity were highest during the summer, and lowest during winter. (2) During blooms, dominant species grew more quickly and had the greatest biomass of the phytoplankton. There were four dominant species and these constituted over 74% of the total phytoplankton cells in different seasons. (3) The growth of dominant species was affected by environmental factors; we termed some "leading factors" as these had the greatest effects. When Lake Chaohu became eutrophic, light, temperature and pH were the leading factors. (4) Although leading factors affect the growth of dominant species, photosynthesis is the most essential variable. The study of the ecophysiology of photosynthesis may reveal the relationship between leading factors and dominant cyanobacteria, and also clarify why a few species of cyanobacteria are able to be dominant during particular seasons. When temperature and pH increased between spring and summer, the photosynthetic rate of M. wesenbergii was greater than that of M. viridis. When temperature and pH decreased between summer and autumn, this was favorable to M. aeruginosa photosynthesis. Similar changes occurred between autumn and winter, and M. viridis replaced M. aeruginosa. Although A. flos-aquae was able to grow at higher temperatures and pH than M. viridis, this filamentous cyanobacterium was not able to adapt to higher light intensity. Light intensity appears to be crucial for these cyanobacteria. Our hypothesis is formulated from common understanding within the natural sciences: questions arising at a higher level of integration (such as ecology or agronomy), often require mechanistic answering at a lower integrative level (such as the ecophysiology of photosynthesis).