The study objective was to evaluate the effects of fish stocking density on the prevalence of pathogens isolated from sixty clinically healthy fishes reared under different densities in floating net-cages in Setiu lagoon. The water temperature, pH, DO, TDS, salinity, water clarity, depth, and coliform concentration, were all determined within the fish cages. The healthy fish samples were randomly collected from 3 sites in cages with low and high stocking densities at each site. The bacteria were isolated from the skin, gills, kidneys, and liver of each fish sample, followed by identification to species level using the VITEK-2 system. The pathogens with beta-hemolysis characteristics were selected for antibiotic susceptibility against the following drugs: AM-10 µg, P-10 U, CL-30 µg, TC-30 µg, CP-5 µg, GM-10 µg, KM-30µg, and SM-10 µg. Water quality parameters showed no differences between the cages of low and high fish densities except for site C. The total number of isolates, microbial species, and the number of pathogens isolated from fish revealed no significant difference between the fish stocked in low and high densities. A total of 25 bacterial species were isolated, which included 14 gram-positive and 11 gram-negative. The (SM) drug application is suspected on this farm.