We investigated presence of zebra mussel, Dreissena polymorpha, which is considered as harmful for two freshwater ecosystems (Omerli Reservoir and Lake Sapanca), in the food preferences of several gobiid species namely; Neogobius melanostomus, Neogobius gymnotrachelus, and Neogobius fluviatilis. In Lake Sapanca, zebra mussel was the dominant food component in the diet of gobiids. However, in Omerli Reservoir, plant with macropyhtes and algea were the dominant food sources both studied gobiids. Intraspecific diet overlap indices showed that gobiid species from the same lake preferred similar food types (S > 0.8). However, when we compared the lakes, the diet overlap index between N.fluviatilis (Lake Sapanca) and N. gymnotrachelus (Omerli Reservoir) was not significant (S= 0.5) which indicates different food choices. The relationships between total length and weight, which had slope values >3 in all but one case, differed significantly between species. One exception was between N. fluviatilis (Lake Sapanca) and N. melanostomus (Omerli Reservoir). In generally, slopes of the relationships in fish species from Lake Sapanca were bigger than those of Omerli Reservoir. This result suggests that gobiids fed with mostly zebra mussel had better weight gain compared to gobiids fed with mostly plant-based food. This study showed that gobiid fishes are an important consumer of zebra mussel and their predation would affect the mussel populations, especially in the ecosystems where zebra mussel is abundant.