The estimation of organic carbon stored in Arctic permafrost and its biogeochemical characteristics are important topics in today’s permafrost research. In particular, large uncertainties and sparse data on the quantity, quality and distribution of permafrost-stored deep organic carbon affect how well carbon cycle models can project permafrost carbon feedbacks to the atmosphere. We studied the organic carbon content of the Alaskan and Siberian Yedoma region, where substantial quantities of organic matter such as peat inclusions, twigs and root fragments, other solid plant remains, and finely distributed plant detritus, were embedded in permafrost soils and in thick sediments over millennia during the late Quaternary. This region is also unique because of its high amount of ground ice and thus vulnerability to thaw and surface subsidence. Rapid inclusion of organic matter into permafrost halted decomposition and resulted in a long-term carbon sink in ice-rich sediments that are tens of meters thick. With this survey we estimated the amount and quality of deep ancient carbon stored in the Alaskan and Siberian Yedoma region. We show that two major sub-reservoirs compose deep frozen organic carbon of the Yedoma region: Yedoma deposits (late Pleistocene ice- and organic-rich silty sediments) and deposits formed in drained thaw-lake basins (generalised as thermokarst deposits). Using a biomarker approach, we revealed that thermokarst deposits are slightly more degraded than Yedoma deposits. Nevertheless, both deposits still show a high risk for microbial reactivation and decomposition to methane or carbon dioxide. Quantitative estimates reveal significant differences to former area estimates of the Yedoma coverage, thickness of the frozen deposits, ground ice content, and organic carbon content. As a result, we suggest a revised total deep permafrost carbon pool for the northern high latitude Yedoma region. This pool has a high range of uncertainty due to full incorporation of statistical uncertainties in each variable used for organic carbon pool calculation by observation-based bootstrapping statistics. In conclusion, we quantified the organic carbon pool to 83+61/-57 Gt for Yedoma deposits and to 128+99/-96 Gt for thermokarst deposits. The total Yedoma region with an organic carbon pool of 211+160/-153 Gt is a substantial amount of thaw-vulnerable and potentially labile organic carbon if the temperature rises in the far north. To reduce the for the first time estimated large quantity uncertainties in the organic carbon pool, we suggest that more data is especially needed on the spatial extent (lateral and thickness) as well as ice wedge content of Yedoma and thermokarst deposits.