Abstract: Objective To understand the genetic characteristics of coxsakievirus A16 (Cox A16) strains isolated in Huzhou, Zhejiang province during 2011-2012. Methods Viral nucleic acids were detected from 538 clinical specimens collected from HFMD cases in Huzhou during 2011-2012 with real-time PCR. Cox A16 RNA positive samples were used for subsequent cell culture. Sequencing and analyses of VP1 encoding gene were performed for 17 Cox A16 isolates. Results The results showed that Cox A16 and EV71 were the major pathogens of HFMD epidemic in Huzhou during 2011-2012. Sequence analysis for VP1 gene of the Cox A16 strains indicated that the viruses' nucleotides and amino acids sequences shared 89.5%-100% and 99.3%-100% homology respectively. The nucleotides sequence of the 17 strains showed a high level of identity to the B1 genotype reference strains. Phylogenetic analysis of the VP1 region showed that all the Cox A16 isolates in Huzhou were clustered within the B1a and B1b evolution branch of B1 genotype. Conclusion Like other Cox A16 strains isolated in China,the major circulating strain of Cox A16 in Huzhou during 2011-2012 belonged to B1 genotype, which could be further classified into Bla and B1b branches.