This dataset describes two 17 m long sediment cores taken from beneath two thermokarst lakes in the Yukechi Alas, Central Yakutia, Russia. The first core was taken from below an Alas thermokarst lake (YU-L7; 61.76397°N, 130.46442°E) and the second core below and Yedoma lake (YU-L15; 61.76086°N, 130.47466°E).The dataset presents biogeochemical and biomarker parameters of sediment cores YU-L7 and YU-L15. Biogeochemical analyses include total carbon (TC) content, total organic carbon (TOC) content, total nitrogen (TN) content. Biomarker parameters include the n-alkane concentration, average chain length (ACL), carbon preference index (CPI), brGDGT concentration, archaeol concentration and the isoGDGT-0 concentration.The n-alkanes were measured in the aliphatic fraction by gas chromatography-mass spectromety using a Trace GC Ultra coupled to a DSQ MS.The branched and isoprenoid glycerol dialkyl glycerol tetraethers, as well as the dialkyl glycerol diether lipid (archaeol) were measured in the NSO fraction using a Shimadzu LC-10AD high-performance liquid chromatograph coupled to a Finnigan TSQ 7000 mass spectrometer via an atmospheric pressure chemical ionization interface.The pH soil is the sediment pH which was assessed by adding 6.12 mL of 0.01 M CaCl~2~ to ~2.5 g dried sediment and measuring with a Multilab 540 (WTW) at 20°C.