We examined the environmental stresses experienced by cyanobacteria living in endolithic gneissic habitats in the Haughton impact structure, Devon Island, Canadian High Arctic (75° N) and compared them with the endolithic habitat at the opposite latitude in the Dry Valleys of Antarctica (76° S). In the Arctic during the summer, there is a period for growth of approximately 2.5 months when temperatures rise above freezing. During this period, freeze–thaw can occur during the diurnal cycle, but freeze–thaw excursions are rare within higher-frequency temperature changes on the scale of minutes, in contrast with the Antarctic Dry Valleys. In the Arctic location rainfall of approximately 3 mm can occur in a single day and provides moisture for endolithic organisms for several days afterwards. This rainfall is an order of magnitude higher than that received in the Dry Valleys over 1 year. In the Dry Valleys, endolithic communities may potentially receive higher levels of ultraviolet radiation than the Arctic location because ozone depletion is more extreme. The less extreme environmental stresses experienced in the Arctic are confirmed by the presence of substantial epilithic growth, in contrast to the Dry Valleys. Despite the more extreme conditions experienced in the Antarctic location, the diversity of organisms within the endolithic habitat, which includes lichen and eukaryotic algal components, is higher than observed at the Arctic location, where genera of cyanobacteria dominate. The lower biodiversity in the Arctic may reflect the higher water flow through the rocks caused by precipitation and the more heterogeneous physical structure of the substrate. The data illustrate an instance in which extreme climate is anti-correlated with microbial biological diversity.