Objectives The characteristic of molecular biology in one strain of Porcine Circovirus Type-4 suspected to be infected by piglets in a farm in Guizhou Province was studied. Methods Nucleic acids were extracted from the piglet multiple system failure syndrome (PMWS)-suspected piglets and PCR method was used to amplify and sequence the full-length of Cap gene in PCV4. Bioinformatics software was used to analyze the Cap gene and its encoded amino acids. Results The nucleotide sequence of Cap gene in PCV4 obtained was 687 bp in length. The DNA sequence corresponding to the start codon and stop codon during transcription was predicted to be ATG and TAA. The homology of nucleotides with the reference strain ranged from 96.2% to 99.1%, and the similarity of encoded amino acids ranged from 89.5% to 96.1%. There was a total of 23 amino acid mutated sites encoded by ORF2, and the mutation sites were mainly concentrated after position 115. The 19 phylogenetic trees of Cap gene in PCV4 collected in this experiment had no spatial and temporal pattern. Conclusions One strain of PCV4 was detected in a suspected piglet with PMWS in a farm in Guizhou Province. The Cap gene of this strain is genetically close to JXYC-2021 in Jiangxi, China, and it was found from the phylogenetic tree that PCV4 has no regional distribution worldwide.