The present study concerned with the issue of the microbiological contamination of fish that result from polluted aquatic environment of fish or contamination due to non hygienic fish handling in the fish markets. Fish Samples of Clarias lazera (Garmout) were collected from Khartoum central market and Khor Aldabaseen. The total viable count of bacteria; and the detection of Escherichia coli, Staphylococcus aureus and Salmonella spp. in the flesh and gills of fish were carried out. Results showed that the mean values of total viable bacterial count of Clarias lazera muscles and gills were significantly different between the two collection sites (P < 0.05). The percentage of presence of bacteria species in the flesh of Clarias lazera collected from Khartoum central market were found to be 28.57%, 0.00% and 28.57% for Escherichia coli, Salmonella spp and Staphylococcus aureus respectively. And The percentage of presence of bacteria species in the flesh of Clarias lazera collected from Khor Aldabaseen were found to be 42.86%, 14.29% and 71.43% for Escherichia coli, Salmonella spp and Staphylococcus aureus respectively. Whereas the calculated percentage of presence of bacteria species in the gills of Clarias lazera collected from Khartoum central market were found to be 42.86%, 28.57% and 42.86% for Escherichia coli, Salmonella spp and Staphylococcus aureus respectively. And the percentage of presence of bacteria species in the gills of Clarias lazera collected from Khor Aldabaseen were found to be 42.86%, 28.57% and 57.14% for Escherichia coli, Salmonella spp and Staphylococcus aureus respectively.
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