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The bacterial flora of the rearing pond water and sediment as well as the gills and intestine of healthy hybrid tilapia cultured in Saudi Arabia was estimated quantitatively and qualitatively, the isolates being identified at genus or species level. Total viable counts of bacteria (measured as colony‐forming units, cfu) were in the range 5.6 ± 0.8 × 103 to 2.4 ± 1.2 × 104 cfu mL−1 in pond water; 9.3 ± 1.1 × 106 to 1.9 ± 1.5 × 108 cfu g−1 in sediment; 7.1 ± 0.7 × 105 to 8.7 ± 1.1 × 106 cfu g−1 in the gills of tilapia; and 3.4 ± 1.8 × 106 to 5.8 ± 0.4 × 107 cfu g−1 in the intestine of tilapia. In total, 15 bacterial genera and 18 species were identified. Pond water and sediment bacteria reflected the bacterial composition in the gills and intestine of tilapia. In contrast to gill bacteria, more diversification was observed in intestinal bacteria. Corynebacterium urealyticum, Shewanella putrefaciens and Aeromonas hydrophila predominated in all samples. In pond water, C. urealyticurn, S. putrefaciens, A. hydrophila, Flavobacterium sp. and Pseudomonas sp. were the most predominant bacterial species (prevalence > 10%), whereas A. hydrophila, C. urealyticum, S. putrefaciens and Escherichia coli were predominant in pond sediment, and C. urealyticum, S. putrefaciens and A. hydrophila were predominant in both the gills and intestine of tilapia.