Impacts are common geologic features on the terrestrial planets throughout the solar system, and on at least Earth and Mars impacts have induced hydrothermal convection. Impact-generated hydrothermal systems have been suggested to possess the same life supporting capability as hydrothermal systems associated with volcanic activity. However, evidence of fossil microbial colonization in impact-generated hydrothermal systems is scarce in the literature. Here we report of fossilized microorganisms in association with cavity-grown hydrothermal minerals from the 458 Ma Lockne impact structure, Sweden. Based on morphological characteristics the fossilized microorganisms are interpreted as fungi. We further infer the kerogenization of the microfossils, and thus the life span of the fungi, to be contemporaneous with the hydrothermal activity and migration of hydrocarbons in the system. Our results from the Lockne impact structure show that hydrothermal systems associated with impact structures can support colonization by microbial life.