Genomic sequence analysis demonstrates that porcine circovirus type 2 (PCV2) isolates are divided into distinct genotypes. Historically, swine herds in the U.S. have been infected with the PCV2a genotype. In 2005, PCV2b was identified in North America and with it increased reports of porcine circovirus disease (PCVD). A differential PCR technique incorporating PCV2 genotype-specific primers was used in the clinical diagnosis of PCVD. A set of 97 diagnostic submissions showed that both PCV2a and PCV2b were present in 25% of clinical samples. The construction of phylogenetic trees using whole genome sequences from diagnostic submissions showed that one isolate, 0737A, was only loosely associated with other PCV2b isolates. Analysis of the variable sites between representative PCV2a and PCV2b DNA sequences and the 0737A sequence, showed that 0737A was a mosaic sequence, with the ORF1 region from PCV2a and ORF2 from PCV2b. This study demonstrates that pigs can be naturally infected with multiple PCV2 genotypes and that PCV2a/PCV2b recombination events occur in the field.