A remarkable biogenic calcite precipitate forms carpets of finely laminated ∼1 mm diameter columns lining fissures within limestone bedrock in the permafrost regions of the northern Yukon. This material, “endostromatolite,” for its laminated morphology and growth hidden within the carbonate rock, is ubiquitous within limestone terrains of the Arctic and grew during the early Holocene hypsithermal. Dissolution on the interior fissure faces is accompanied by biomineralization of the opposing faces; a previously unrecognized weathering process in permafrost regions. Occurrence is restricted to outcrops with a southern orientation in permafrost regions, in this case, from the Ogilvie Mountains, northern Yukon. Growth occurs in water-saturated talik during periods of permafrost degradation during insolation maxima. Their enriched δ13C values (–1.7‰ to 11.4‰) are generated in a methanogenic environment during anaerobic degradation of soil-derived organic carbon. A paleotemperature signal extracted from the δ18O values demonstrates that growth occurred during a hypsithermal period with an average summer air temperature 7 ± 2 °C higher than today. Corrected radiocarbon age measurements of the calcite and organic matter preserved within the endostromatolites indicate that biomineralization occurred during the late Pleistocene – early Holocene hypsithermal event. Profiles along the columns document late Pleistocene climate improvement, with maximum warmth coincident with the insolation maximum for 65°N, followed by cooling and end of growth in the mid to late Holocene.