Abstract: Objective To analyze the genetic characterization of enterovirus type71 ( EV71 )associated with hand foot and mouth disease (HFMD) epidemics in Jilin province,during 2009-2010.Methods Randomly selected 31 representative EV71 strains from the eases of 8 prefectures to amplify and sequences of VP1 genes of EV71 strains,and analyzed with Bioedit and Mega4.0 program.Results All representative 31 EV71 strains belong to C4a subgenotype,the homology of nucleotide in VP1 region among the 31 EV71 strains were 94.5%-100.0%,and were clustered into 5 transmission chains respectively.25 strains out of 31 strains were associated with a predominant transmission chain,and circulating in 8 prefectures,while other 6 strains clustered into 4 lineages.Conclusion Multiple transmission chains of EV71 C4a subgenotype were co-circulating in Jilin province during 2009-2010,and a predominant transmission chain was circulating in 8 prefectures,associated with HFMD outbreaks of Jilin province.