Aerobic anoxygenic phototrophic bacteria (AAPB) is significant for productivity of freshwater ecosystems. However, it remains unclear that the distribution characteristics and ecological assembly process of AAPB in low illumination freshwater basins at present. Here, we track the diversity, abundance, spatial variations, ecological process and community interaction of bacteria and AAPB in sediment of the Three Gorges Reservoir (TGR), which is a typical low radiation freshwater reservoir, based on high-throughput sequencing of 16S rRNA and pufM gene and the qPCR of pufM gene. In TGR, the qPCR of AAPB ranged between (2.21±0.44) × 10 4 and (9.98±0.30) × 10 7 pufM gene copies/g, and Rhodobacteraceae-like pufM sequences were determined, and the sequences of Methylobacteriaceae-liked and Sphingomonadaceae-liked also existed here. The qPCR of AAPB was increasing while the Chao1 and Shannon indices decreased from the upstream to the downstream. However, the contribution of geographical and environmental factor is little to the spatial difference of community. The stochastic process played a dominant role in the aggregation and replacement of bacterial and AAPB communities, among which the most contribution was dispersal limitation. The network analysis showed that most of the keystone species were not the most abundant, which could not to be ignored in this unique environment. For pufM gene microbial network, Tabrizicola spp. and Gemmobacter spp. were the hubs for modules. In addition, these unclassified taxa based on pufM gene, also known as “microbial dark matter”, has important implications for ecosystem processes . The results obtained here provide help for further understanding distribution characteristics and ecological processes of bacteria and AAPB in TGR, a typical low illumination area.