The aromatic hydrocarbon fraction of the surface sediment in the west and east part of Taihu Lake was analyzed by GC-MS. As a result, a series of long chain fatty acid methyl esters was first found. Distribution of the carbon number of fatty acid methyl esters in the samples was from C_14 to C-34 maximizing at C_16 with a strong even to odd carbon preference. Their mass spectrum char- acteristics are that base peaks were M/Z 74, 87 and characteristic ions were M/Z 143, 199, M~+, M-43~+. These ion existence was confirmed by fragmenting analyses of fatty acid methy esters. The origin of the long chain fatty acid methy esters in the sediment of Taihu Lake was also stud- ied, which may be related to biochemical process. The result showed that the long chain fatty acid methyl esters was probably an important biological marker to study the acidity of the lake sediment.