Objective:To analyze the genetic characteristic of VP1 gene of coxsackievirus A16 (CA16) strains isolated from Jiangsu Province in 2012. Methods:A total of 14 CA16 strains isolats were selected to conduct VP1 gene amplification by using specific primers,and then sequenced and analyzed by bioinformatics software. The homology and phylogenetic analysis were conducted between the 14 isolates and other CA16 strains downloaded from Genbank,based on the sequence of VP1 gene. Results:The sequence analysis showed that the homogeneity of the nucleotide and amino acid of VP1 gene were 90.5%~100% and 98.7%~100% among 14 isolated CA16 strains,respectively. The homologies of nucleotide and amino acid of VP1 gene were 75.5%~76.7% and 91.6%~92.3% among the prototype(G10),respectively. All of the CA16 isolated strains from Jiangsu Prorice in 2012 were genogroup B and they were divided into 2 branches:B1a and B1b. Conclusion:The transmission mode was showed to be the dominant subgenotype of B1b and the secondary subgenotype of B1a,and co-circulated together. Both two subgenotypes showed close phylogenetic relationship in their own subgenotype,respectively.