Certain marine diatoms can be harmful to seaweed cultivation farms, resulting in loss of yield and quality. Diatoms are exposed to viral attack; to date, more than 20 diatom-infecting viruses have been isolated and characterized to different extents. Nevertheless, no data have been reported on viruses infecting the harmful bloom-forming diatom Asteroplanus karianus, which causes bleaching of cultured Pyropia. In this study, we successfully isolated a novel virus that infects A. karianus from the sediment of the Ariake Sound, which is famous for its nori cultivation. The virion was 21 nm in diameter and exhibited apparent host cell lysis over 10 days post inoculation. Moreover, using degenerate PCR targeting the RNA-dependent RNA polymerase (RdRp) domain, ssRNA virus sequences were detected from a natural diatom bloom population, which included A. karianus, collected in the Ariake Sound. The phylogenetic analysis showed that the detected sequence was monophyletic with diatom-infecting ssRNA virus members at a bootstrap value of 85%. These results indicated that viruses infecting A. karianus are present in the Ariake Sound and may play a role in decreasing the diatom populations in natural environments.