Mercury is a toxic element acquired by animals through feeding which can accumulate within food chains through biomagnification. This possesses particular risks to higher trophic levels and may unduly impact marine foraging species or individuals. The fish-eating bat (Myotis vivesi Menegaux, 1901) inhabits islands in the Gulf of California and can act as a predator in the marine environment. A predominantly marine diet and a high trophic position increase the risk of mercury exposure owing to increased bioaccumulation. Using molecular techniques to reconstruct diet, we show that M. vivesi regularly feeds on small fishes and crustaceans, particularly on the Californian anchovy (Engraulis mordax Girard, 1854) and a krill species (Nyctiphanes simplex Hansen, 1911). Additionally, we identify significant interannual variation in diet composition within this population, but measured levels of total mercury in faecal samples were not related to dietary diversity or trophic level.