Porcine circovirus 3 (PCV3) is a newly emerged circovirus discovered in 2016, and since then is threatening the swine industry worldwide. In this study, we evaluated the presence of different PCV3 strains in swine herds from Brazil. PCV3 was detected by qPCR in different samples from different life stages. Sequencing was performed with seventeen positive samples. This study reported the coinfection of different PCV3 strains in one animal. This study provides insights into the genetic diversity of PCV3 strains circulating in the Brazilian swine herds.