Betanodaviruses are the causative agents of viral nervous necrosis (VNN) or viral encephalopathy and retinopathy (VER) in cultured marine fish. A total of 131 apparently healthy fish from 30 species were collected in two geographically remote aquaculture areas, Yashima Bay (Kagawa Prefecture) and Tamanoura Bay (Nagasaki Prefecture), in Japan. The brains of fish were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect the coat protein gene of betanodavirus. In Yashima Bay, two and 13 of 20 cultured fish were positive for nodavirus in RT-PCR and nested PCR, respectively, and four of five wild fish were positive only in nested PCR. In Tamanoura Bay, 28 and 99 of 106 wild fish were positive for the virus in RT-PCR and nested PCR, respectively. All the sequences of the nested PCR products (177 nt) from 27 fish species (10 cultured and 17 wild) were highly homologous to each other (99-100%) and were closely related to that of the known betanodavirus, redspotted grouper nervous necrosis virus (RGNNV). These results illustrate that large populations of cultured and wild marine fish in aquaculture areas are subclinically infected with genetically closely related betanodaviruses, suggesting an importance of such infected fish as a carrier or reservoir of betanodaviruses.