Abstract: Five isolates of encephalomyocarditis virus were isolated from clinical tissue samples originated from suspected cases of intensive pig farms. Two isolates of them (BJC3 and HB1) were systematically identified. The results showed that round virus particles with diameter of 27 nm were observed by immune electron microscopy. The physicochemical character tests indicated that the isolates BJC3 and HB1 were not able to endure acid and insensitive to chloroform. However, the two isolates had different sensitivity to trypsin treatment. Exposed under 60 ℃ for 1 h, the viruses could be inactivated and protection of bivalent cation at temperature of 50 ℃ was negligible. The specific fluorescence was observed in the cytoplasm of BHK21 cells infected with the isolates by indirect fluorescence assay using polyclonal antibody against EMCV. The VP1 gene and partial segment of 3D gene of the two isolates were amplified by RTPCR and sequenced. Sequence analysis revealed that the nucleotide identity of VP1 gene was 99.49% and the predicted amino acid identity was 98.46% among the two isolates. The nucleotide identity of VP1 genes between EMCV strains in GenBank database and the isolates ranged from 81.61% to 99.59%. Correspondingly, the amino acid identity was above 95.5%. The identity of 3D gene amplified of both the nucleotide and amino acid was 100% among the two isolates and other EMCV strains.Phylogenetic analysis based on the nucleotide sequences of VP1 gene of EMCV showed that the two isolates were located on the backbone of the phylogenetic tree, with lesser variation. These results suggest that EMCV infection exist in pig farms in China.