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The Chinampas are important historically and represent a special agroecosystem that has been sustainable for many years. However, their agricultural potential has currently decreased mainly because of irrigation with waste water from Mexico City, leading to progressive salinity and alkalinity problems and the subsequent general alteration on the agroecosystem. Chemical composition of the main groups of lipid molecules in anthropogenic organic soil from Xochimilco and Tlahuac Municipalities (Mexico) were investigated. The analysis performed included physicochemical characteristics of the soil and the distribution analysis of free alkanes and fatty acids. The successive accumulation stages of organic materials in these anthropogenic organic soils represent a source of irregular distribution in organic carbon, likewise the concentration of lipid extracts differed noticeably with depth. There is a vertical variability, where hydromorphic environment has played a key role in this variability. The major compounds identified in the soil lipid extracts by gas chromatography-mass spectrometry include series of linear and satured alkanes, fatty acids, as well as individual components such as sterols and hopanes. Most of the lipid components in these soil seem to have a biogenic origin (higher plants and microorganism biomass).