To explore the changes in the microbial community structure during the recovery process of an anammox reactor after a temperature shock, the 454-pyrosequencing technique was used. The temperature shock reduced the nitrogen removal rate up to 92% compared to that just before the temperature shock, and it took 70 days to recover a similar nitrogen removal rate to that before the temperature shock (ca. 0.30 g N L-1 d(-1)). Pyrosequencing results indicated that microbial diversity in the reactor decreased as the reactor progressively recovered from the temperature shock. Anammox bacteria were accounted as 6%, 35% and 46% of total sequence reads in samples taken 13, 45 and 166 days after the temperature shock. These results were in agreement with N-removal performance results and anammox activity measured in the reactor during the recovery process. An anammox specific primer was used to precisely determine the anammox species in the biomass samples. (C) 2015 Elsevier Ltd. All rights reserved.