Abstract: The diversity of bacteria flora in skin, buccal cavity and gills of Lutjanus agennes, Pseudotolithus elongatus, Sphyraena barracuda from of Lagos lagoon were examined and compared. Different identification procedure and techniques (colonial morphology, isolation and culturing) were used to determine if pathogenic bacteria groups were present. Gram staining, motility, sugar fermentation as well as biochemical tests were also carried out. The bacteria isolated were Klebsiella spp. Proteus spp. Staphylococcus aureus, Citrobacter spp. Streptococcus pyogenes, Salmonella spp. Micrococcus spp. Bacillus licheniformis, Alcaligenes spp. Pseudomonas aerugenosa, Shigella spp. Enterobacter aerogenes, Escherichia coli and Serratia spp. from the skin, buccal cavity and the gill of randomly selected species. The bacterial count of L. agennes was highest in the buccal cavity (cfu = 10.9±0.2, f<0.05) than gills (cfu = 6.2±0.1, f<0.05) and skin (cfu = 4.2±0.3, f<0.05), P. elongates highest also in buccal cavity (cfu = 11.02±0.53, f<0.05) than gills (cfu = 6.2±0.2, f<0.05) and skin (cfu = 4.6±0.2, f<0.05), S. barracuda highest also in buccal cavity (cfu = 8.6±0.5, f<0.05) than gills (cfu = 5.6±0.1, f<0.05) and skin (cfu = 5.3±0.1, f<0.05). The bacteria flora isolated from the water sample were not totally different from the ones isolated from the fish except for Clostridium perfringenes, Staphylococcus epidermidis and Vibrio parahaemolyticus. The bacteria assemblage wereassemblages were of public health significance.