Abstract: Post-weaning multisystemie wasting syndrome (PMWS) is an emerging disease in swine.Porcine circovirus type 2 (PCV2) has been associated with the PMWS.Two PCV2 strains were isolated from pigs showing signs of PMWS in Fujian Province.They were denominated FUQING0401 and PUTIAN0401.the sequencing of 2 PCV2 strains along with the phylogenetie analysis of these strains and those of 12 PCV2 sequences published in GenBank were compared.Sequence analysis of the complete genome indicated that the Fujian PCV2 strains were closely related to each other but also to other PCV2 strains originating from Canada, USA, Europe and China.Sequence analysis of ORF1 genes of the 2 strains revealed that the extent of nucleotide homologous was 97.5 %.The amino acid sequences alignment of the PCV2 replicatase protein identified 6 amino acid heterogeneity.Capsid protein genes of PUTIAN0401 and FUQING0401 homologous rate was 99.7%, and the amino acid homologous rate was 98.7%.Phylogenetic analysis revealed that the 14 strains could be divided into several clusters, but the homologous rate was different from 91.6%to 99.9%.The two strains from Fujian were spread in small groupings and an association with geographic origin could not be established.