Porcine circovirus type 2 (PCV2) has been recognized as a causative agent of porcine circovirus-associated diseases (PCVAD) affecting the global swine industry for more than three decades. The high mutation rate of PCV2 can lead to rapid evolution and emergence of novel PCV2 strains. In this study, we investigated the genetic diversity of PCV2 strains circulating in Thailand between 2019-2020. From 734 samples (145 farms), 396 (54.0%) samples obtained from 118 farms were positive for PCV2. Of these, whole-genome sequences of 51 Thai PCV2 strains were analyzed and assigned to PCV2d (86.3%) and PCV2b (13.7%). The complete genomic analysis also revealed an intergenotypic recombinant virus between PCV2b and PCV2d. Our findings and viral sequence dataset provide essential information on the genetic diversity of PCV2, including the evidence of novel intergenotypic recombination of PCV2 in Thailand.