A survey to determine the pathogenic bacterial strains of an important commercial capture fish, Oreochromis niloticus in an Egyptian fish farm was conducted. One strain presumptively identified as Shewanella putrefaciens was isolated from the fish and identified by a biochemical test, API20NE system and 16S rRNA gene. Intraperitoneal (I.P) challenge by S. putrefaciens revealed its pathogenicity with 50% mortality. The infected fish showed skin hemorrhage, fin rot and shallow necrotizing ulcers on the skin with congestion and enlargement of the liver, spleen and kidneys. The antibiogram of S. putrefaciens revealed its sensitivity to ciprofloxacin, norfloxacin, nalidixic acid, streptomycin, gentamycin, oxytetracyclin and sulfamethoxazole. Complete resistance to cephazolin and fusidic acid was recorded. Histological changes in the liver of infected O. niloticus included hepatocyte degeneration, fatty vacuolation in liver cells, Kupffer cell increase, hemolysis with infiltration in blood vessels, deposition of hemosiderin associated with the liver blood vessels and necrosis hepatocytes in the fatty liver tissue. The results concluded that the S. putrefaciens should be considered as an opportunistic pathogen for fish, which had caused fish infections, diseases with septicemia and mortality in O. niloticus.