As Arctic warming continues and permafrost degrades, more organic carbon (OC) will be decomposed in high northern latitudes. Still, uncertainties remain in the quality and quantity of OC stored in permafrost. This study presents OC data from permafrost deposits on the Baldwin Peninsula, West-Alaska. We analyzed cryostratigraphical, biogeochemical and biomarker parameters of yedoma- and drained thermokarst lake basin (DTLB) deposits as well as thermokarst lake sediments to identify the size and quality of OC pools in ice-rich permafrost. Here we show that two thirds of soil OC in this region are stored in frozen DTLB deposits and that the lake sediments have the highest volumetric OC content. The n-alkane distribution shows, however, that OC stored in yedoma is of higher quality than that stored in DTLB deposits. These findings highlight the importance of molecular OC analysis for determining the potential future greenhouse gas emissions from thawing permafrost.