Based on the complete genomic sequence of PCV-2 in GenBank, two sets of primers were designed, and genomic DNA was extracted from PK-15 cell inoculated with pathogenic materials of piglets with PMWS. Complete genomic sequences of two isolates from Guangdong Province were amplified. The two sequences were compared with that of other PCV-2 isolates in GenBank with the DNAStar software, and a phylogenetic tree of PCV-2 strains was drawn. The length of the complete genome of GZ and ZS strains was (1 767) bp; nucleotide similarity of the complete genome among two strains was 77.0%; but nucleotide similarity of ORF1 only was 57.7%, but which of ORF2 was 99.1% among two strais; nucleotide similarity of the complete genome among ZS strain and other strains were from 95.7%-99.5%, and were from 74.2%-77.1% among GZ strain and other strains.