Porcine circovirus type 3 (PCV3) is a novel circovirus that was firstly detected in the USA. PCV3 is associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure and cardiac and multisystemic inflammation. Latterly, PCV3 was detected in Guangxi, China. Forty-one of 108 (37.96%) samples and nine of 47 (19.14%) samples were PCV3 positive in pig farms and pig slaughter houses, respectively. Three PCV3 strains were sequenced and designated PCV3-China/GX2016-1, PCV3-China/GX2016-2 and PCV3-China/GX2016-3. The complete genome of PCV3-China/GX2016-2 and PCV3-China/GX2016-3 is both 2,000 bp in length, while PCV3-China/GX2016-1 is of 1,999 bp and has a G deletion at position of 1,155 in its genome. The complete genome and capsid nucleotide of the three PCV3 strains identified in this study shared 97.5%-99.4% and 96.7%-99.1% identities with that of the other PCV3 strains available in NCBI, respectively. Phylogenetic analysis based on complete genome and capsid gene of 35 PCV3 strains showed that the three PCV3 sequences from Guangxi Province were divided into two clusters. The results of this study contribute to the understanding of PCV3 molecular epidemiology.