The aim of this study was to identify some bacterial (Vibrio cholerae, Listonella anguillarum, Yersinia ruckeri, Aeromonas hydrophila, Aeromonas sobria and Aeromonas caviae) and viral (infectious pancreatic necrosis virus, viral hemorrhagical septicemia virus and infectious hematopoietic virus) pathogens by comparing the bacteriological culture and molecular methods with histopathological examination of various tissues seen in Pearl mullet from freshwater rivers inflowing to the Van lake. Accordingly, bacterial and viral agents were detected in a total of 180 pearl mullet samples by bacteriological culture and Real-Time PCR methods. The samples were collected from six different freshwater rivers that flows to Van lake by random sampling. In the study, Vibrio cholerae, Listonella anguillarum, Yersinia ruckeri, Infectious Pancreatic Necrosis Virus, Viral Hemorrhagic Septicemia Virus and Infectious Hematopoietic Necrosis Virus could not be isolated. However, Aeromonas spp. was identified by bacteriological culture and Real Time PCR methods at 22.22% and 53.33% respectively. The most dominant species was observed to be Aeromonas hydrophila among all identified Aeromonas spp. In histopathological examinations of Aeromonas spp. positive samples, disorders were detected in gill, liver, spleen and kidney tissues. Telangiectasia, edema, hyperplasia and adhesions were observed on the seconder laminates of gills. In liver, the order of the Remak cords were disarranged, and degenerative changes formed in hepatocytes. Melano-macrophages loaded with hemosiderin were intensively detected in all Aeromonas positive samples. As a result, the risk of motile Aeromonas infections in the pearl mullet living in freshwaters flowing into the Van lake is still highly and this could lead to serious adverse effects on human health. To prevent these effects, attention must be paid to hygiene conditions and cold chain in fish served for consumption, the and rivers must be protected from pollution.