Compound specific isotope analysis of lake sediments is a powerful tool in deciphering evidence of changing climatic and paleoenvironmental conditions through time. Isotopic analysis of Lake El’gygytgyn pilot sediment cores, PG1351 and LZ1029, have contributed increased insight into paleoenvironmental interpretations regarding conditions of permanent ice cover and water column anoxia at the lake over the past 250 kyr. Bulk sediment δ15N was measured as a proxy for denitrification and a possible indicator for water column anoxia intensity. However, it appears that insufficient quantities of water column nitrate to fuel denitrification make its correlation with anoxia intensity ineffective. In pilot core LZ1029, compound-specific δ13C of alkanes, fatty acids, and alcohols were analyzed to determine the changing sources of organic matter as well as the source of a strong negative isotopic shift in the bulk sediment δ13C (-26‰ to -33‰) over the past 50 kyr. Results indicate that the majority of alkanes, fatty acids, and alcohols are long chain compounds consistent with a terrestrial plant origin, with increased aquatic contribution during the local last glacial maximum (LLGM). Among the compound classes examined, only the mid chain fatty acids display a strong LLGM depletion (δ13C = -43‰). Short chain fatty acids exhibit an LLGM depletion (δ13C = -35‰) similar to bulk sediment δ13C, while the δ13C trend of long chain alkanes, fatty acids, and alcohols differ from the bulk sediment δ13C trend, suggesting an autochthonous source of bulk isotope depletion. Evidence of methane cycling exists only in the presence and isotopic value of diplopterol (LLGM δ13C = -93.4‰), a biomarker for aerobic oxidation of methane. Two compounds indicative of archaeal lipids were present at considerable concentrations during the LLGM (394 and 668 µg/g TOC), but without the extreme negative δ13C associated with methanogenesis and methanotrophy. These results suggest insufficient generation of methane in the lake to have derived from such a large anaerobic archaeal methanogen community suggesting that archaea are not acting entirely as methanogens. Furthermore, it appears unlikely that a significant anoxic layer existed in the water column of Lake El’gygytgyn during the past ~50kyr. The results of this work will be applied to ongoing investigations on the newest cores from Lake El’gygytgyn, which represent the past 3.5 Myr.