Abstract: Porcine Circovirus type 2 (PCV2) is one of the most important swine pathogens of economic importance. To understand the genetic diversity of Porcine Circovirus type 2 (PCV2) in South China, 49 PCV2 sequences from South China were compared to 58 other references sequences. Researchers found that the nucleotide similarity among all South China isolates ranged from 93.7-100%. Most of them were classified into PCV2b-1A/1B cluster but the rest mapped to clusters PCV2b-1C, PCV2a-2E or PCV2a-2F. The data contribute to the understanding of molecular variation of PCV2 in South China.