This study evaluated the microbial quality of farmed tilapia from seven fresh water farms of Cagayan which were endorsed by the Bureau Fisheries and Aquatic Resources Provincial Office of Cagayan. The study utilized a Mixed Method of analysis where the profile of fish farms and microbial quality of tilapia harvested from the fish farms were quantitatively described while a Focus Grouped Discussion was done to determine farm practices of the fish farm owners. Interview, observation techniques and document reviews were also done to validate some responses provided by the participants in the FGD. Results of the bacterial culture conducted revealed the presence of different bacterial isolates from the fish samples which were found to be pathogenic and may be due to poor fish farm practices. Further, the results of the study showed that most fish farm owners do not comply to practice basic sanitary and hygienic protocols as endorsed by BFAR. While the bacteria load levels detected from the fish samples were within the acceptable limit as prescribed by the Food and Drug Administration of the Department of Health, some fish farms were detected to have high bacterial loads in as much as the harvested fishes from these sites are concerned because of the use of contaminated source of water supply. The study strongly recommends BFAR to conduct stricter monitoring and implement sanitary and hygienic practices in the fish farms of Cagayan to avoid food poisoning and intoxication once fishes like tilapia are consumed. Consumers are likewise advised to cook properly fishes cultured in fish farms.