Industrial effluents, agricultural runoff, and municipal wastewaters contain unknown substances and complex mixtures that are released into the environment and can lead to contamination of surface and subsurface waters. Such activities have endangered the existence of ecosystems and their inhabitants. Changes in the genome caused by genotoxic agents led to mutations and pose a burden to the populations of fish species. In the present study, we have used the alkaline Comet assay to detect the genotoxicity in Suez pufferfish (Lagocephalus suezensis) sampled from two different gulfs (Iskenderun and Mersin Bay), Northeastern Mediterranean. At the end of the study, the damage frequency (%), arbitrary unit and genetic damage index (%) were evaluated in gill and liver cells of L. suezensis by comet assay. The DNA damage in the gill and liver cells of L. suezensis in the present study were observed with a higher level of DNA damage in gill cells compared to liver cells in both the Iskenderun and Mersin Bays. The highest level of DNA damage (55.01±1.02%), arbitrary unit (143.01±7.21) and genetic damage index (1.43±0.07 %) were found in gill cells of L. suezensis from Mersin Bay. Statistically significant differences were found between DNA damage, Arbitrary unit and genetic damage index values of the two locations (p < 0.001). In conclusion, this study indicates that comet assay gives sensitive results in monitoring the pollution, especially the pollution of the gulf, and thus it might be used as a standard method in regularly monitoring the pollution of the coastal ecosystem.