In recent times, increase in human interference on aquatic environment has tremendously interfere on the biota composition which nonetheless contribute to health status of fish. This study was undertaken to identify the bacterial flora from thirty-six life samples of C. nigrodigitatus and O. niloticus collected from two environments; fresh water (Osun River) and Brackish water (Lagos Lagoon) South-western Nigeria, Sub Saharan Africa. Specimen were collected from gills, intestines and skins of fish species and homogenized in 105 serial dilutions with distilled water. The specimens were cultured on Nutrient agar using pour plate method at 37oC for 24 hours. Two-way ANOVA was used to calculate mean count at P<0.05 significant level. Bacterial flora occurrence from the two species are: Streptococcus spp (10%), Vibrio spp (3%), Escherichia coli (15%), Micrococcus spp (3%), Aeromonas spp (7%), Bacillius spp (3%), Spirillium spp (6%), Proteus spp (4%), Staphylococcus spp (18%), Pseudomonas spp (14%), Aerococcus spp (5%), Lactobacillius spp (1%), Alcogenes spp (1%), Citrobacter spp (1%), Fusobacterium spp (2%), Flexibacter spp (3%), Flavobacterium spp (2%), Salmonella spp (1%), klebisella spp (1%). Total bacteria count found in each sample from Lagos lagoon was higher than that of samples from Osun River, which may be attributed to dense urbanization around brackish water environment as a result of higher degree of pollution.