The permafrost region approximately makes up one quarter of the land surface of the Northern Hemisphere. Its soil organic carbon (OC) pool is estimated to be 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 OC pool is of major concern. In particular, the size and quality of OC stocks in permafrost deposits are of interest since they determine availability of carbon to microbial decomposition and may significantly influence the outcome of permafrost carbon feedbacks to climate. The aims of this study were to characterize organic matter (OM) stored in Holocene (thermokarst) and Late Pleistocene (Yedoma) permafrost deposits in regard to the quantity and quality of OC. To address the research questions, an interdisciplinary multi-proxy approach was applied on permafrost deposits sampled on Sobo-Sise Island in the Lena Delta (northeast Siberia). A four meters long core was taken from a baydzerakh hill on a Yedoma upland and two thermokarst exposures were sampled, one located in a thermokarst depression and the other on a rapidly eroding Yedoma slope. The methodological approach consisted of sedimentological (ice content, bulk density), geochemical (total OC (TOC), total OC : nitrogen (C/N) ratio), hydrochemical (dissolved OC (DOC), acetates), stable isotopes (δ13C, δ18O, δ2H) and organic geochemical parameters (n-alkanes, n-fatty acids, hopanes, and biomarker indices, i.e. average chain length (ACL), carbon preference index (CPI), and higher-plant fatty-acid index (HPFA)). Furthermore, ages of 15 samples were estimated with radiocarbon dating. The Yedoma upland deposits had larger and more frequent peat inclusions and higher ice contents than the thermokarst profiles. Radiocarbon age determination of the Yedoma upland sequence revealed stratigraphically unsorted Late Pleistocene deposits, and the thermokarst profiles showed Holocene ages. Larger amounts of OC were sequestered in the Yedoma upland deposits than in the thermokarst profiles. TOC had mean values of 11 wt% and 50 kg/m3 in the Yedoma upland core and mean values lower than 5 wt% and 28 kg/m3 in the thermokarst profiles. DOC concentrations were also higher in the Yedoma upland deposits with a mean value of 680 mg/l (maximum value of 2600mg/l), while the thermokarst profiles had mean values below 200 mg/l. Most indicators of OM degradation like the abundance of n-alkanes, the acetate concentration, the C/N ratio, and the CPI index indicated better preserved OM in the Yedoma upland deposits compared to the thermokarst profiles. δ13C, n-fatty acid concentration and abundances of hopanes revealed no clear differences between thermokarst and Yedoma upland deposits. This study revealed a large and relatively well preserved carbon pool stored in permafrost deposits of the Lena Delta, suggesting an important carbon feedback to climate if exposed to degradation processes. Particularly high OM content and low degradation were evidenced in the Yedoma upland deposits, which are expected to be more susceptible to future thermokarst degradation. Depending on the environmental conditions, the microbial community and degradation regime that will establish, OM degradation could be restrained or facilitated.