Rainbow trout which is one of the most produced species in Turkey is affected by many bacterial diseases that cause physiological disorders and economically important losses. Especially pathological disorders in the muscle cause intense loss in fish processing and packaging facilities. The aim of this study is determining the cause of physiological disorders such as reddish brown patches and hemorrhages on processed or unprocessed fish products. Petechial hemorrhages and ecchymosis that formed on the skin of the fish were observed caused by Listonella anguillarum. Also, Lactococcus garvieae isolated from fish samples with hemorrhagic lesions, abscess fillet with blood and deep ulcers. It is determined that L.garvieae cause more severe hemorrhagic septicemia than L.anguillarum and the disease was observed as acute and chronic cases. The abscess in the muscle and hemorrhages formed in the abdominal wall are serious problems that were noticed during and after the processing of fillets and smoked fillets. Hemorrhages in the muscle are observed as red patches in the fillet and after the smoking process, these patches turn into brown marks which are undesirable organoleptic properties in the processing industry and the serving size fish can not be evaluated. Besides, greenish yellow patches on the abdominal walls caused by the overproduction of bile and exploding off the gall bladder which may be related to metabolic disorders or bacterial and parasitic diseases. These fish are also not able to used, separated as discarded and cause economically intolerable loss in the industry.