Few studies have been conducted to explore the community composition in denitrifying biocathode. Herein, the microbial communities of denitrifying biocathodes yielding current of 1 mA (reactor C1) and 1.5 mA (reactor C2) were characterized by 454 pyrosequencing. The nitrate removal efficiencies in C1 and C2 were about 93 and 85%, respectively. The optimization of data generated high-quality sequences of 18509 in C1 and 14857 in C2. Proteobacteria was the predominant phylum, and Bacteroidetes, Chloroflexi, and Planctomycetes were the subdominant groups. Classes of Alphaproteobacteria, Anaerolineae, and Phycisphaerae may benefit the performance of current production and nitrate removal. Twenty-nine dominant operational taxonomic units (OTUs) accounted for 64 and 65% of sequences in C1 and C2, respectively. A denitrifying pathway was constructed based on the phylogenetic analysis and function inferring of the dominant OTUs. Obviously, the 454 pyrosequencing provided a high-resolution profile of bacteria community in denitrifying biocathode.