This is the first study exploring the effects of persistent Cr(VI) treatment on microbial communities and function as well as the process efficiency of an A(2)O system. The inhibitory effect was clearly higher at a high Cr(VI) concentration than a low Cr(VI) concentration, and different Cr(VI) concentrations had distinct effects on the microbial communities as well as on the performance efficiency of the system. Functional annotation analysis indicated that Cr(VI) stress inhibited most of the metabolic pathway and functional genes of the microbial communities, especially those involved in the denitrification pathway. Network analysis was used to investigate the co-occurrence patterns between denitrification genes and microbial taxa; the results indicated that microorganisms with functional genes had high diversity and were adversely affected by Cr(VI) exposure. This study is the first to establish a relationship between Cr(VI) stress and microbial communities and function as well as to determine the underlying mechanisms and roles of Cr(VI) in A(2)O sludge.