The occurrence of orange/pinkish colored lesions in the adductor muscle of Yesso scallops Patinopecten yessoensis has been known for many years in Japan; however, determination of the causative agent has not been adequately investigated. ​Histological examination of affected scallops in southern Hokkaido typically revealed intense host responses: hemocyte infiltration, an abundance of necrotic hemocytes, lysis of muscle fibers and in some instances melanin deposits when the lesions occurred adjacent to the shell. ​Microbiota analysis showed that Francisella halioticida was dominant in the lesions, and in situ hybridization using F. halioticida specific probes also confirmed the presence of this bacterium within the lesions. ​A F. halioticida specific PCR assay detected this bacterium in the majority of scallop lesions tested. ​Subsequently, three bacterial isolates were obtained from scallop lesions on modified Eugon agar supplemented with antibiotics, and these bacterial isolates were found to be F. halioticida by 16S rRNA and rpoB gene sequences. ​These results suggest that infection with F. halioticida is the most likely cause of the adductor muscle lesions observed in Yesso scallops. ​Field surveys conducted in 2017 of scallops cultured in southern Hokkaido showed that the presence of adductor muscle lesions putatively caused by F. halioticida was significantly related to mortalities and poor growth of scallops