Abstract: Use of organic fertilizers has become very common in the modern piscicultural practices; vermicompost is a new addition to the list of such fertilizers. The efficacy of vermicompost was better than the other fertilizers both in keeping the hydro-biological parameters of treated waters in favourable ranges as well as in maximizing the fish growth. However, its effect on the pathogenic bacterial profile of treated waters is not known. To accomplish this objective, an experiment was performed in 5.54×6.15 m size ponds stocked with three species of Indian major carps viz. catla (Catla catla Ham.), rohu (Labeo rohita Ham.) and mrigal (Cirrhinus mrigala Ham.) at 30 fish per pond in 3:4:3 ratios, respectively. Six treatments viz. a control without any treatment (T1), pig manure at 4,000 kg ha–1 year–1 (T2), poultry manure at 6,000 kg ha–1 year–1 (T3), cow dung at 10,000 kg ha–1 year–1 (T4), vermicompost at 10,000 kg ha–1 year–1 (T5) and vermicompost at 15,000 kg ha–1 year–1 (T6) were used to monitor their effect on the pathogenic bacterial populations in the treated pond waters. One fourth doses of fertilizers were applied 15 days prior to the fish stocking and the remaining doses were given at fortnightly intervals; the supplementary feed was given at 2% of the body weight of fishes. The pure culture of bacterial isolates segregated from the pond sediments were identified by primary, secondary and tertiary tests and confirmed for their pathogenicity through in vitro and in vivo tests. Overall, seven gram negative pathogenic bacterial strains (viz. Aeromonas hydrophila, Escherichia coli, Enterobacter aerogens, Pseudomonas fluorescens, Klebsiella oxytoca, Pseudomonas aeruginosa and Shigella sp.) and three gram positive strains (viz. Micrococcus luteus, Staphylococcus aureus and Staphylococcus sp.) were isolated from the pond waters treated with different manures. The in vitro and in vivo tests confirmed the pathogenic nature of these bacteria. The abundances of the heterotrophic pathogenic bacteria were minimal in the pond waters treated with vermicompost at 10,000 kg ha–1 year–1 followed by those treated with vermicompost at 15,000 kg ha–1 year–1; the abundances of pathogenic bacteria were higher in waters treated with other fertilizers including under the control treatment. Under other than these two vermicompost treatments, the abundances of pathogenic bacteria were variable depending upon the bacterium-fertilizer type. On the basis of these results, vermicompost at 10,000 kg ha–1 year–1 seemed to be the best among the five organic fertilizer treatments in controlling the abundance of pathogenic bacteria in the treated pond waters.