Abstract: Objective To understand the genetic characteristics of VP1 region of Coxsackie A16 virus(Cox A16) isolated from hand foot and mouth disease(HFMD) patients in Zhejiang province during 2008-2013. Methods Reverse transcription-polymerase chain reaction(RT-PCR) was conduct to amplify the VP1 region genes of Cox A16 isolated from clinical specimens(stool, herpes fluid and throat swab). Homologous comparison and phylogenetic analysis of Cox A16 strains were performed by using reference Cox A16 strain and Cox A16 strains isolated from other areas of China. Results A total of 81 Cox A16 strains were isolated, and they shared 88.7%-100% homology of nucleotide and 97.8%-100% homology of amino acid of VP1 region. Compared with the prototype strain of Cox A16(G-10/RSA/1951), the homologies of nucleotide and amino acid were 61.9%-65.1% and 90.1%-91.7%, respectively. The phylogenetic tree indicated that all the 81 Cox A16 strains belonged to gene subtype B1(B1a and B1b). Conclusion The Cox A16 strains isolated in Zhejiang from 208 to 2013 belonged to gene subtype B1 and could be further classified as B1a and B1b.