The permafrost region approximately makes up one quarter of the land surface of the Northern Hemisphere. Its soil organic carbon pool is estimated to be about twice the size of carbon in the modern atmosphere. In the context of climate warming, understanding the processes that are linked to permafrost thaw and its effects on the organic carbon pool is of major concern. In particular, permafrost carbon quality characteristics are of interest since they determine availability of carbon to microbial decomposition and may significantly influence the outcome of permafrost carbon feedbacks to climate. Located at the coastlines of the Laptev Sea in north-eastern Siberia, the Lena Delta accounts to the largest deltas worldwide. Climatic and environmental conditions in this region during the late Pleistocene favored the formation of ice-rich silt deposits penetrated by large ice wedges, so called Yedoma deposits. Yedoma formations offer a unique opportunity to gain knowledge about the quantity and quality of organic matter stored in permafrost deposits as well as the effects of thawing processes on the organic carbon pool. In our approach we used sedimentological (ice content, bulk density) and geochemical parameters (total organic carbon (TOC), dissolved organic carbon (DOC), stable isotopes (δ13C, δ18O, δ2H), organic carbon to nitrogen ratio (C/N)), as well as molecular biomarkers (n-alkanes, n-fatty acids, and biomarker indices, i.e., average chain length (ACL), carbon preference index (CPI), and higher-plant fatty-acid index (HPFA)). Here we found higher concentrations of organic carbon in Yedoma compared to thermokarst basin deposits. The concentrations of DOC, TOC and total n-alkanes clearly was higher in Yedoma deposits than in thermokarst sediments. The CPI values for n-alkanes and n-fatty-acids show a clear increasing trend from thermokarst towards Yedoma, indicating higher degradation in thermokarst deposits and better conservation of OM in Yedoma, and the HPFA index is lower for Yedoma than for thermokarst, hence, suggesting better preservation of organic-matter in thermokarst basin deposits. In conclusion, the amount of organic carbon stored in the Yedoma permafrost deposits proved to be clearly higher compared to that stored in thermokarst. Moreover, the indices for organic-matter quality indicated less degradation of organic-matter in Yedoma deposits and more degraded conditions for organic matter in thermokarst depressions. Generally. the high quantity of the conserved organic-matter stored in Yedoma permafrost deposits underline the vulnerability of this carbon pool when exposed to thawing processes.