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 falty acid methyl esters was first found. Distribution of the carbon number of fatty acid methyl esters in the samples was from C₁₄ to C₃₄ maximizing at C₁₆ with a strong even to odd carbon preference.Their mass spectrum characteristics 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 studied, which may be related to biochemical process. The result showed that the long chain fatly acid methyl esters was probably an important biological marker to study the acidity of the lake sediment.