<p>Porcine circovirus 3 (PCV3) has emerged as a significant pathogen associated with various clinical manifestations affecting global swine populations. To investigate the prevalence and molecular characteristics of PCV3 strains, we collected 11,194 tissue samples from pigs across 650 farms of varying breeding scales in 18 cities of Henan province from March 2022 to December 2024. Detection of PCV3 was performed using a validated real-time quantitative PCR assay. The results showed that the total positive rate of PCV3 was 9.25% (1035/11,194), and PCV3 was detected on pig farms in 18 cities of Henan Province. The complete genome sequences of six PCV3 strains and the ORF2 gene sequences of four PCV3 strains were determined and analyzed. These 10 PCV3 strains shared 98% to 99.7% nucleotide sequence identity in ORF2 with PCV3 reference strains. The complete ORF2 gene sequences of these 10 PCV3 strains shared 98.4% to 99.8% nucleotide sequence identity with each other, and the encoded proteins shared 98.1% to 100% amino sequence acid identity. Phylogenetic analysis based on the ORF2 gene indicated that all 10 sequenced PCV3 strains belonged to genotype PCV3b. Notably, two amino acid mutations were identified in predicted B cell epitopes within the Cap protein of the these strains, which may affect the immunogenicity of PCV3. These data contribute to our understanding of the molecular epidemiology and evolution of PCV3 and provide a foundation for the prevention and control of PCV3 and other PCVs.</p>