The polar desert is one of the most extreme environments on Earth. Endolithic organisms can escape or mitigate the hazards of the polar desert by using the resources available in the interior of rocks. We examined endolithic communities within crystalline rocks that have undergone shock metamorphism as a result of an asteroid or comet impact. Specifically, we present a characterization of the heterotrophic endolithic community and its environment in the interior of impact-shocked gneisses and their host polymict breccia from the Haughton impact structure on Devon Island, Nunavut, Canadian High Arctic. Microbiological colonization of impact-shocked rocks is facilitated by impact-induced fissures and cavities, which occur throughout the samples, the walls of which are lined with high abundances of biologically important elements owing to the partial volatilization of minerals within the rock during the impact. 27 heterotrophic bacteria were isolated from these shocked rocks and were identified by 16S rDNA sequencing. The isolates from the shocked gneiss and the host breccia are similar to each other, and to other heterotrophic communities isolated from polar environments, suggesting that the interiors of the rocks are colonized by microorganisms from the surrounding country rocks and soils. Inductively coupled plasma–atomic emission spectroscopy (ICP-AES), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) analysis were used to identify the chemical composition of the shocked materials and to document the in situ growth of microbes in their interiors. The identification of these heterotrophic communities within impact-shocked crystalline rocks extends our knowledge of the habitable biosphere on Earth. The colonization of the interiors of these samples has astrobiological applications both for considering terrestrial, microbiological contamination of meteorites from the Antarctic ice sheet and for investigating possible habitats for microbial organisms on the early Earth, and more speculatively, on Mars and other planetary bodies.