Lethal impact of the bacterium Francisella halioticida on Yesso scallops Mizuhopecten yessoensis has been experimentally demonstrated, but epidemiological information for this bacterium infection in scallop farms has been limited. Thus, the present study conducted a monthly epidemiological survey for 4 years on adult scallops ear-hung from 2017 to 2020 on a scallop farm in northern Japan. As a result, the prevalence of F. halioticida in low temperature period increased for all year groups, but any association with scallop mortality was recognized. On the other hand, in the 2017–2019 year groups, increase of the prevalence and rapid declines of scallop survival were recognized in high-temperature periods. Additionally, overall survival in these year groups were apparently lower than the 2020 year group without increase of the prevalence in high-temperature period, suggesting that infection of F. halioticida in high-temperature periods may be associated with mortality of scallops. Abscess lesions in the adductor muscle were found to be associated with F. halioticida infection, but not always formed in infected scallops. Thus, presence of abscess lesions may serve as an indicator for francisellosis, but not necessarily a definitive symptom for this disease.