For the first time, high-throughput sequencing was employed to investigate the microbial communities of the biofilm in an autohydrogenotrophic denitrifying bio-ceramsite reactor. 30,418 and 39,178 bacterial 16S rRNA gene sequences were obtained from biofilm Samples C1 and C2 in the reactor under HRT 16h, pH 7.0 and HRT 48h, pH 9.0 conditions. Results showed that the mainly reported autohydrogenotrophic denitrifying phyla Proteo bacteria, Firmicutes and classes Gammaproteobacteria, Alphaproteobacteria, Bacilli were all detected in the reactor, and their high relative abundances demonstrated they played key roles in the autohydrogenotrophic denitrification process, suggesting that this bio-ceramsite reactor presented better denitrification performance. The heatmap analysis illustrated that the largest genus in Sample Cl was Acinetobacter, while Planomicrobium was the largest genus in Sample C2. In addition, the reported hydrogenotrophic denitrifying genera Ochrobactrum, Paracoccus, Pseudomonas, Hydrogenophaga, and Thauera were always observed in the reactor, suggesting that this bio-ceramsite reactor exhibited autohydrogenotrophic denitrifying capacity to convert nitrate to nitrogen gas. This work might add some new insights into microbial communities in autohydrogenotrophic denitrification process. (C) 2015 Elsevier Ltd. All rights reserved.