Quantitative analyses of bacterial flora associated with the intestine of Macrobrachium vollenhovenii, sediment and water from Epe lagoon and Badagry Creek were carried out. Total viable counts (TVC) of bacteria in the intestine of the prawn ranged from 5.7 ± 0.3 × 10 7 to 8.1 ± 0.3 × 10 7 (cfu g -1 ) and 2.8 ± 0.6 × 10 7 to 5.3 ± 0.4 × 10 7 (cfu g -1 ) at Epe lagoon and Badagry Creek respectively. There were significant variation (p<0.05) in the total viable counts of bacteria isolated at both aquatic systems. Altogether, 11 gram negative bacteria genera were identified and found to be common to the lagoon environment. Escherichia coli, Aeromonas hydrophila, Salmonella typhi and Pseudomonas aeruginosa were the most abundant species in the samples from Epe Lagoon while Escherichia coli, Aeromonas hydrophila, Proteus vulgaris and Pseudomonas aeruginosa were predominant in Badagry Creek. It was noteworthy that Citrobacter sp. was not found in Epe lagoon while Salmonella typhi and Vibrio cholerae was absent in Badagry Creek. This study provides amongst others baseline information on bacteria of wild stock of Macrobrachium vollenhovenii thus providing needed thrust when farming the species.