[Objective] Maar lake is a special type of Crater Lake. Huguangyan Maar Lake was formed about 140 k?160 k years ago, fully closed, and has not yet been affected by human activities, where abundant and novel microbial species might dwell as reported previously. Aerobic anoxygenic phototrophic bacteria (AAPB) is a functional bacterial group with long evolution history in Earth possessing unique physiological and ecological characteristics. To date, our knowledge about AAPB distribution in Maar Lake is still blank. [Methods] Here, by constructing and analyzing six clone libraries of the photosynthetic reaction center pufM gene from total DNA and RNA, respectively, with 1 m, 5 m, and 12 m water layers in Huguangyan Maar Lake, and combining quantitative Real-time PCR, we studied AAPB’s distribution, phylogenetic diversity and the proportion in the total bacteria in different water layers. The results of coverage value and rarefaction curves of six libraries showed that AAPB diversity was sampled well for the purpose of revealing the diversity of main AAPB groups in each water layer. [Results] BLAST analysis showed that pufM sequences in Maar Lake were 80%?93% similar to public sequences. Diversity index indicated that the AAPB diversity in surface and deep layers was similar, whereas diversity in the intermediate layer was lowest. In view of total RNA and DNA data, pufM RNA diversity was higher than that of DNA. Phylogenetic and statistical analysis revealed that 49.43% sequences are fell into the OTUs 21?24 which were closely related to β-proteobacteria and represent dominated AAPB groups. Quantitative PCR results showed that the percentage of AAPB in total bacteria in 1 m water layer reached a highest value of 38.06%, whereas only 0.85% and 9.54% in 5 m and 12 m, respectively. [Conclusion] Huguangyan Maar Lake is occupied by rich and diverse AAPB groups.