Porcine circoviruses (PCVs) type 1 (PCV1) and type 2 (PCV2) show high levels of nucleotide similarity, but PCV1 is considered non-pathogenic and PCV2 has been associated with several disease outcomes in pigs, mainly postweaning multisystemic wasting syndrome (PMWS). After exploring different topologies of the origin of PCVs, it was concluded that PCV1 and PCV2 seem to have a common origin. On the other hand, PCV2 could be divided into two groups (1 and 2) and eight clusters (1A to 1C and 2A to 2E), but none of those was apparently associated with disease status or geographic area. When phylogenetic trees constructed with the whole PCV2 genome, the cap or the rep genes were compared, some incongruence was identified. The possible existence of recombination was evaluated and cluster 1B was found to have a possible recombinant origin. Selective pressure was detected in all parts of the PCV2 genome, especially in the rep gene. Finally, the cap gene was the more suitable phylogenetic and epidemiological marker for PCV2, despite the fact that the virus can undergo recombination mainly within the first part of the rep region.