This dataset describs 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 the branched glyerol diakyl glyerol tetraether (brGDGT) concentrations from sediment cores YUL7 and YU-L15 which are given in µg/g sediment.The branched glycerol dialkyl glycerol tetraethers 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.