Abstract: Objective To understand the genetic evolution and recombination of enterovirus 71 (EV71) isolates in Huzhou during 2011-2012. Methods A total of 2 EV71 isolates were used for whole genome sequencing and the sequences were aligned with other genotypes of EV71 and prototype strains of EV-A. Phylogenetic tree was constructed with software Mega 4.0 and similarity analysis was done with software Simplot 3.5.1. The recombination confirmation were performed. Results The phylogenetic analysis based on P1 regions revealed that the EV71 isolated in Huzhou during 2011-2012 belonged to C4a in genotype C4. Similarity analysis and phylogenetic analysis based on the P1, P2, P3 genomic regions confirmed the recombination between EV71 genotypes C and Cox A16, 14 and 4 at region 2B. Conclusion EV71 isolated in Huzhou during 2011-2012 belonged to C4a in genotype C4, which was the predominant virus genotype circulating in the mainland of China since 2004,and the intratypic recombination was found in EV71 subgenotype C4.