The lack of pathogen genome information is one of the main reasons for the slow progress of oyster disease research. In order to identify more oyster-associated viruses, based on the previously obtained viromic data of oysters (Crassostrea hongkongensis
) cultured in multiple locations along the coast of the South China Sea, after quality control, assembly, and species annotation of the sequencing data, we selected the putative circovirus genome sequences for the construction of the phylogenetic tree, genome comparison, protein domain analysis, structure prediction and virus abundance analysis, which provides references for the research of oyster disease. The results show that five viral sequences clustered with known circoviruses in a large branch, indicating that they are members of the Circoviridae family. The five viral genome sequences all contained replication protein genes, with the highest similarity to a replication protein sequence of arthropod circovirus. The five sequences and seven other public database sequences formed an independent sub-branch. Viruses on this branch were mostly from animal-related samples. Based on the domain analysis (SMART), replicase conserved domains were identified in most sequences.