Swine manure was typical for the combined pollution of heavy metals and antibiotics. The effects of widely used veterinary antibiotic chlortetracycline (CTC), Cu and their combination on swine manure anaerobic digestion performance and microbial community have never been investigated. Thus, four 2 L anaerobic digestion reactors were established including reactor A (control), B (CTC spiked by 0.5 g/kg dry weight, dw), C (Cu spiked by 5 g/kg dw) and D (combination of CTC, 0.5 g/kg dw, and Cu, 5 g/kg dw), and dynamics of bacterial and archaeal community structure was investigated using high throughput sequencing method. Results showed that addition of CTC and Cu separately could increase the total biogas production by 21.6% and 15.8%, respectively, while combination of CTC and Cu severely inhibited anaerobic digestion (by 30.3%). Furthermore, corresponding to different stages and reactors, four kinds of microbes including bacteria and archaea were described in detail, and the effects of CTC, Cu and their combinationmainly occurred at hydrolysis and acidification phases. The addition of Cu alone changed the dynamics of archaeal community significantly. It was genus Methanomassiliicoccus that dominated at the active methane production for A, B and D, while it was genus Methanobrevibacter and Methanoculleus for C. (C) 2017 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V.