Microbial quality of Labeo rohita, Cyprinus carpio and Clarias batrachus collected from the markets of Kathmandu valley was evaluated. 9 freshwater fish (skin, gills, intestine) were sampled and were analyzed for Total Plate Count (TPC), Total Coliform Count (TCC) and Total Fecal Coliform Count (TFCC). The average TPC ranged from 4.1 x 107 to 1.02 x 108 cfu/gm, with the highest count in C. batrachus and the lowest in C. carpio, whereas the organ wise load was the highest in intestine with 1.3 x 108 cfu/gm and the lowest in skin with 1.02 x 107 cfu/gm. The highest TCC and TFCC was found in C. carpio and C. batrachus respectively, whereas organ wise distribution showed the highest count in intestine for both TCC and TFCC. The pathogens isolated from the samples were Escherichia coli, Staphylococcus aureus, Coagulase negative Staphylococcus (CoNS), Vibrio cholerae, Salmonella Typhi and S. Paratyphi. E. coli was isolated from 67% of L. rohita, 44.44% of C. carpio and 66.67% of C. batrachus. S. aureus was isolated from 44.44% of both L. rohita and C. batrachus whereas 55.55% of C. carpio. CoNS were isolated from 33.33% of L. rohita, 22.22% of C. carpio and 33.33% of C. batrachus. S. Typhi was isolated from 11.11% of C. carpio and 22.22% of C. batrachus. S. Paratyphi was isolated from 11.11% of both L. rohita and C. batrachus, V. cholerae was isolated from 11.11% of L. rohita, 33.33% of C. carpio and 22.22% of C. batrachus. The observation of this study showed higher bacterial load in all of the fishes above the acceptance level and presence of Total Coliform, Fecal Coliform and potential human pathogens suggests that the microbial quality of the fish available in the market is not satisfactory. Hence, the fishes possess a threat to public health safety and there is an urgent need to improve the Quality Control and Quality Assurance Systems for fish markets of Kathmandu valley.