The Zhejiang-Fujian coastal mud, a typical muddy deposit off the East Chinese continent, is a complex sink of organic matters sourced from both the Changjiang River and the western Pacific,which carry a large amount of information on climatic changes and anthropogenic activities. Lipid biomarkers, such as free fatty acids, produced by plants,algae,phytoplankton and bacteria have been used increasingly to identify the specific sources of organic matter in marine sediments. The distribution pattern of free fatty acids over the last 160 years in the sediment coresDZ-28 (28.63°N, 122.36°E; water depth 52.8m),and DZ-41 (28.07°N, 121.95°E; water depth 42.2 m)from Zhejiang-Fujian coastal mud area is investigated in the present paper. Results show that the free fatty acids are dominated by the marine autochthonous fatty acids derived from planktonic and bacterial sources, and followed by a small amount of allochthonous higher plant-derived fatty acids from the land. In response to the changes in the intensities of the East Asia Monsoon,the Kuroshio intrusion and the Pacific Decadal Oscillation phase,the amounts of marine free fatty acids are significantly higher in the 20th century than those in the 19th and abnormally high values found in the period from the late 1970s to early 1990s. Meanwhile, heavy floods (such as those in 1998,1954 and 1931 mentioned in literatures) from the whole of the Changjiang River catchment may lead to the sharp increase in terrestrial higher plant-derived free fatty acids instead of the decrease in marine autochthonous free fatty acids. Furthermore, human activities have become the dominating factor that caused the durative increase in total free fatty acids in particular the marine autochthonous ones since the late 1960s. Our study based on the indicators of free fatty acid further reveals that the construction of the Three Gorges Dam has inhibited to certain extent the growth of diatoms, and the i-C_(15:0)% can be used effectively to invert the history of the hypoxia events in this mud area. The low-oxygen events have been in a trend of increase since 1950s followed by a more dramatic one after the 1980s.