Based on the molecular distribution of bound fatty acid (BFA) compound classes in core sediments of Lake Dianchi combined with the compound-specific δ(13)C values of the straight-chain BFAs, origin and vertical changes of organic matters in the sediments were investigated. The results indicated a significant change of BFA sources over the past 700 years. Contrast to the low concentrations of the terrestrial BFAs, the abundance of BFAs derived from the plankton/bacteria in the top sections (1944-recent) was more than 80%. The increasing proportions of the branched and unsaturated BFAs in total fatty acids were closely correlated with the heavy eutrophication and the frequent algal blooms in the decades. Furthermore, the positive shift of δ (13)C of C16 and C18 (~2‰) in the upper section might be an indicator of the excess phytoplankton productivity. However, it was found that the plankton/bacteria-derived BFAs were more easily degraded during the early diagenetic process. The special compound carbon isotopic compositions of the long straight-chain BFAs (C24 and C26) in the sediments showed a depletion of heavier δ (13)C values (ca. -30‰) in the midsections (1559-1787), reflecting a relatively growing contribution of C3 plants to C4 plants or that C4 plant growth was inhibited in cold and arid climates during the period.