Abstract: Oysters with filter feeding habits enrich a large number of pathogens including viruses in water, like a very valuable virus bank. To conduct an in-depth research on oyster-related viruses, we sequeced the Hong Kong oyster (Crassostrea hongkongensis) collected along the South China coast. After the quality control, assembly and taxonomy annotation of the sequencing data, we selected five genomic sequences which were identified as Microviridae for multi-dimensional analyses, such as host prediction, open reading frame and gene function prediction, phylogeny and three-dimensional structure prediction of major capsid proteins, evolutionary association between major capsid proteins and external scaffold proteins, as well as virus abundance analysis. The results show that the hosts of the five viruses were all Escherichia; one of the virus genome sequences was clustered in Bullavirinae branch, which indicates that it is a member of the subfamily; the other four genome sequences were not clustered into any known subfamilies so they should belong to a single unclassified subfamily; the relationship between the evolutionary tree of the main capsid proteins and external scaffold proteins indicates that the evolution rules of the two proteins were different.