Porcine circovirus type 3 (PCV3) has recently been detected in pigs worldwide, with similar clinical manifestations to porcine circovirus-associated disease (PCVAD) from porcine circovirus type 2 (PCV2) infection. Here, we report the identification and molecular epidemiology of PCV3 in swine in Thailand from clinical samples retrieved from 2006 to 2017. The epidemiological data revealed co-infection with PCV2, PRRSV, and PCV2/PRRSV was common in our samples. Circulating PCV3 from this study shared a high similarity of nucleotide and deduced amino acid sequences of the partial capsid gene (96.7%-100% and 96.7%-100% respectively), indicated the genetic stability of PCV3 in Thailand. Phylogenetic analysis based on the capsid gene revealed scatter clustering with current PCV3 having no relation to the geographical origin of the virus strains. In this retrospective study, results have demonstrated that PCV3 has spread extensively within Thai swine from as early as 2006 and may also be involved in PRDC and PCVAD.