Many Korean rockfish farms (Sebastes schlegeli) have suffered from a disease causing high mortalities, since outbreaks of furunculosis first occurred in 2008. The aims of this study were to investigate the causal agent of the disease as well as the epidemiological aspects of its occurrence. Rockfish and low-value fish which are used as feed in rockfish farms were sampled and examined for isolation of the causal agent of the disease. All isolates derived from the rockfish were non pigmented, relatively slow-growing bacteria, which were characterized as atypical Aeromonas salmonicida. In particular, vapA gene sequences of the isolated bacteria were most closely related to A. salmonicida. Some of the sampled low-value fish, including big head croaker, Japanese anchovy, and Konoshiro gizzard shad, were infected with atypical A. salmonicida as well. In this study, a total of 22 isolates of A. salmonicida were each determined to be partially resistant to amoxicillin and to oxytetracycline and trimethoprim/sulfamethoxazole. The mean value generated by normalized resistance interpretive (NRI) analysis for florfenicol was 36.6mm, with a standard deviation (SD) of 2.2mm. Using a 2.0 SD limit, the wild type cut off value was ≥32mm, indicating that our isolates were all classified as wild type strains for florfenicol. This study indicates that low-value fish used as feed in the sea-cage rockfish farms are a key source of furunculosis, which may cause continuous disease incidence since the first outbreaks.