A total of 453 strains of Coxsackievirus A16 (CV-A16) were screened out of 1,509 hand-foot-mouth disease (HFMD) samples collected in Taizhou during the period from 2010 to 2013. And between first quarter of 2011 and first quarter of 2013, an outbreak of CV-A16 was found among the HFMD sufferers in Taizhou. Phylogenic analysis of VP1 sequences indicated a major CV-A16 sub-group in Taizhou, whose change pattern of effective population sizes was found to be similar to the pattern of the actual percentage changes of CV-A16 during the outbreak over the same period. More importantly, the sub-group all displayed a Leu (L) to Met (M) mutation at site-23 of capsid VP1 which might be correlated with the outbreak of CV-A16 in Taizhou. J. Med. Virol. 88:202–210, 2016. © 2015 Wiley Periodicals, Inc.