The geno-variation and genetic evolution of the ORF3 gene of porcine epidemic diarrhea viruses (PEDV) prevailing in China were studied.Phylogenetic analysis of the ORF3 gene from two representative PEDV isolates from Zhejiang area and 65 PEDV reference strains from other area in China were conducted.The results showed that the 67 ORF3 sequences were clustered into four groups.The strains obtained from Zhejiang in the study fell into G4-2 subgroup,which included the majority of strains studied.The newly obtained strains in this study were highly homologue with the CH-S strain,with a nucleotide identity of 98.4%-98.5% and a deduced amino acid identity of 99.1%-99.6%.The ORF3 gene of strains isolated from south China during 2011 and 2012 constituted G1 group,which had identities of 95.0% to 97.2% in nucleotide and unique nine nucleotide variations compared with other strains.In summary,the strains from Zhejiang area and most other strains studied were clustered into the G4-2 group,while the strains from Southern China were clustered into the G1 group,indicating that there were two different genotypes of PEDV prevailing in China during 2011 and 2012.