Aerobic anoxygenic phototrophic (AAP) bacteria are widely distributed in marine and freshwater ecosystems. The aims of this study were to investigate the diversity and abundance of AAP bacteria in cyanobacterial bloom-forming eutrophic lakes and to study the association of AAP bacteria with the bloom-forming cyanobacteria. Analysis of pufM gene (the light-reaction center gene) clone libraries indicated that in eutrophic lakes (Lake Taihu and Lake Chaohu, China) with cyanobacterium Microcystis blooms, the AAP bacteria were related to members of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In Lake Taihu and Lake Chaohu, Alphaproteobacteria accounted for 81.5% and 75.0% of Microcystis-associated AAP bacteria, respectively, and 84.6% and 72.5% of free-living AAP bacteria, respectively. The predominance of Alphaproteobacteria in the two lakes was different from the previously reported predominance of Betaproteobacteria in freshwater lakes. Quantitative real-time PCR analysis indicated that in Lake Taihu and Lake Chaohu, AAP bacteria represented an important part of the bacterial community associated with Microcystis, and the abundance of Microcystis-associated AAP bacteria (18.3% and 11.7%, respectively) was higher than that of free-living AAP bacteria (5.1% and 7.9%, respectively). The abundance of AAP bacteria in the two bloom-forming lakes was higher than the previously reported level in other eutrophic freshwater bodies.