Aerobic anoxygenic phototrophic bacteria (AAPB) are photoheterotrophic microbes and play a significant role in carbon cycle in aquatic ecosystems. However, the effect of carbon source on the community structure of AAPB remains unknown presently. This study determined the influence of three carbon sources, glucose, sodium pyruvate and yeast extract common used in microbe isolation and culture on total bacteria and AAPB community structures of Lake Ulansuhai, using denaturing gradient gel electrophoresis based on the genes of 16S rDNA and pufM of photosynthetic reaction center respectively. The results showed that diversity and richness of total bacteria community had been enhanced while those of AAPB community been improved previous to 14 days then decreased, after inducing by different carbon sources for 7-21days. Among the three carbon sources, sodium pyruvate best increased the richness and diversity of both total bacteria and AAPB. Sequencing and phylogenetic analysis revealed that some taxonomic strains were discovered which failed to be determined before induction by carbon source and moreover the abundance of some strains harboring specific carbon metabolism were greatly elevated. These results may promote the appreciation for the function and significance of AAPB and provide the basis for their enrichment, isolation and culture.