Clostridium species is considered a foodborne anaerobic pathogen popular in fish. The current study aimed to detect Clostridium species prevalence in fish and freshwater collected from three different Egyptian fish farms. One hundred and eighty samples were collected from the gills and intestines of tilapia, catfish, and Dennis, and 30 water samples were collected from the corresponding farms of sampled fish. A bacteriological examination was conducted to identify different Clostridium species in fish and water. The overall prevalence of Clostridium species in fish was 28.3% (51/180). The prevalence of Clostridium species in tilapia was 30% (18/60), in catfish, was 31.6% (19/60), and in Dennis was 23.3% (14/60). The overall prevalence of Clostridium species in water was 56.6% (17/30). Biochemically, the Clostridium species were identified as Clostridium sporogenes, Clostridium perfringens and Clostridium bifermentans. C. sporogenes was detected by 16.6%, 20% from intestine and gills of tilapia, 16.6%, 13.3% from intestine and gills of catfish, 6.6%, 16.6% from intestine and gills of dennis, 16.6% from water. C. bifermentans was detected by 10%, 13.3% from intestine and gills of tilapia, 13.3%, 20% from intestine and gills of catfish, 10%, 13.3% from intestine and gills of dennis, 13.3% from water. C. perfringens was detected by 26.6% from water. In conclusion, tilapia, catfish, and Dennis can be potentially contaminated with C. bifermentans and C. sporogenes additionally C. perfringens was detected in water of fresh fish farms