Abstract: In this study, the composition and concentration of fatty acid biomarkers in columnar sediment samples at depths of 4 435 m (western cliff, station D109) and 4 568 m (eastern cliff, station S02) from the abyss of the northern Yap Trench were determined, and the sources of the fatty acids and distribution characteristics in the sediment samples were analyzed. The results showed that 25 fatty acids were identified at both sediment samples, with a carbon number of 12-24, mainly in medium-chain and short-chain fatty acids. The distribution characteristics of different types and forms of fatty acids in the sediments of the two stations were significantly different. The total fatty acid content in the sediment from station D109 on the west side was higher, with an average concentration of 88.41 μg/g, mainly in bound form; and the total fatty acid content in the sediment of S02 station on the east side was 66.68 μg/g, mainly in free form. The concentrations of fatty acids in the surface sediments of the two stations were the highest, and 18∶0 and 16∶0 were the most abundant fatty acids. The fatty acids of the sediment from the two stations were derived from the ocean, including algal sources, bacterial sources and zooplankton sources. δ¹³C values of the fatty acids reached as low as −136.48‰ and −78.83‰ in the sediment from the two stations, indicating the existence of microbial biochemical processes using methane as a carbon source. The content of 18∶1ω7 in the sediments of station D109 on the west side of the abyss was higher, which were more significantly affected by deep-sea hydrothermal fluid, and the proportion of fatty acids in total organic carbon increases with the increase of depth, therefore the sediments of station D109 were fresher. The variations of fatty acid content in the two sediment samples were affected by “funnel effect” of the trench, change of carbonate compensation depth and fatty acid degradation. This study would provide basic information on fatty acid biomarkers in the abyssal environment of the northern Yap Trench, which is helpful for deeper understanding of the biogeochemical cycle of deep-sea organic carbon.