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Asteroid and comet impacts on Earth are commonly viewed as agents of ecosystem destruction, be it on local or global scales. However, for some microbial communities, impacts may represent an opportunity for habitat formation as some substrates are rendered more suitable for colonization when processed by impacts. We describe how heavily shocked gneissic crystalline basement rocks exposed at the Haughton impact structure, Devon Island, Nunavut, Arctic Canada, are hosts to endolithic photosynthetic microorganisms in significantly greater abundance than lesser-shocked or unshocked gneisses. Two factors contribute to this enhancement: (a) increased porosity due to impact fracturing and differential mineral vaporization, and (b) increased translucence due to the selective vaporization of opaque mineral phases. Using biological ultraviolet radiation dosimetry, and by measuring the concentrations of photoprotective compounds, we demonstrate that a covering of 0.8 mm of shocked gneiss can provide substantial protection from ultraviolet radiation, reducing the inactivation of Bacillus subtilis spores by 2 orders of magnitude. The colonisation of the shocked habitat represents a potential mechanism for pioneer microorganisms to invade an impact structure in the earliest stages of post-impact primary succession. The communities are analogous to the endolithic communities associated with sedimentary rocks in Antarctica, but because they occur in shocked crystalline rocks, they illustrate a mechanism for the creation of microbial habitats on planetary surfaces that do not have exposed sedimentary units. This might have been the case on early Earth. The data have implications for the microhabitats in which biological signatures might be sought on Mars.