Abstract: Biodiversity of the functional bacteria in surface water (0.5 m) in summer in Bohai Sea(BH), Bohai Strait (BHW) and North Yellow (BHH) Sea was studied by 16S rDNA clone library. Ecological distribution of aerobic anoxygenic phototrophic bacteria(AAPB) of the three typical sites in BH, BHW and BHH was analysed by clone libraries of RbcS-mc pufM gene which coding photosynthetic reaction composite center. The results showed that Rhodobacteraceae of -3 Proteobacteria with high relative abundance was the dominant AAPB bacterial flora which was prevalent in the study area. Among the three typical sites, the AAPB microbial community structure of site BH was relatively abundant, including -3、-4、-6 Proteobacteria; Sites BHW and BHH were relatively unitary, both contained -3 Proteobacteria. In addition, research has shown that the BH area was the highest summer temperature and minimum salinity in the three study sites, more conducive to the growth of AAPB community and state. Unidentified bacteria had the highest proportion which suggested that an abundance of unknown AAPB bacterial flora were existed in this sea area, there are worthy of further research and development.