This study was conducted to investigate the status and population dynamics of porcine circovirus type 2(PCV2) in Korea and to assess the molecular evolutionary pattern of the two biologically important, overlapping open reading frames, the ORF1 and ORF3 genes. A wide range of PCV2 genomic sequences (entire genome, ORF1, ORF2 and ORF3) collected between 2001 and 2010 were analyzed using the Bayesian Markov chain Monte Carlo and maximum-likelihood approaches. These techniques identified the PCV2d genotype and the 2Ek cluster of PCV2a in Korea for the first time. Second, the genotypic shift of PCV2b dominating over PCV2a likely occurred between 2002 and 2004 due to a population expansion of PCV2b. In the context of positive Darwinian selection, the results uncovered independent evolutionary patterns in the ORF3 gene compared to the overlapping ORF1 gene and new sites in the viral ORFs/proteins that might relate to differences in the biological properties of the PCV2 groups.