The diarrhoea of pigs, in particular, for the newborns, is very harmful to the pig industry. Porcine circovirus-like virus (Po-Circo-like (PCL) virus) is a circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus. Two PCL virus strains, with severe diarrhoea and hemorrhagic enteritis, have been found in two different pig farms in Guangdong province, China. Subsequently, the full genomes of two strains (PCL virus GD06 and PCL virus GD09) were sequenced. The two PCL viruses contains 3942 nucleotides and 3925 nucleotides, which vary from the genomes of other PCL virus strains with 3912, 3923, and 3942 nucleotides. Besides, the nucleotide identities between two strains and other strains of PCL viruses and Bo-Circo-like virus/CH were 78%-89%. A multiple sequence alignment of these strains showed a similarity of 86.2%-94.4% for the Rep gene sequence and 89.4%-97.7% for the Rep protein sequence. This study found that 9.5% (4/42) of diarrhoea samples and 11.8% (2/17) of pig farms were positive for PCL virus, suggesting that PCL virus may already be widespread in Pig farms in China. Further research on the pathogenicity and epidemiology of PCL virus is required.