In autumn 2009, the first outbreak of the shellfish-killing dinoflagellate Heterocapsa circularisquama bloom was recorded in a small lagoon, Lake Kamo, located on Sado Isl., Niigata Prefecture, Japan. At the time, the fisheries damage on the oyster culture due to the bloom was estimated at about JPY 190 million. Also in summer 2010, H. circularisquama formed a bloom in Lake Kamo, but in this case, no oyster kill was recorded. In the present study, we measured the temporal change in the abundance of viruses causing lysis of H. circularisquama and compared it with the host dynamics. We checked the host specificity and virus sensitivity of the isolated virus clones and host clones, respectively. Different types of host and virus clone dominantly coexisted in this lake, and the intraspecies host specificity of each HcRNAV clone isolated in Lake Kamo, 2010, agreed well with the host range predicted based on the deduced amino acid sequence of the major capsid protein (MCP). Considering the contemporary appearance of the host and virus, viral infection was assumed to be one of the factors affecting the dynamics of H. circularisquama population in this lake.