Dissolved alkanes and dissolved fatty acids were collected from Qingmuguan underground river in July, October 2013. By gas chromatography-mass spectrometer (GC-MS), alkanes and fatty acids were quantitatively analyzed. The results showed that average contents of alkanes and fatty acids were 1 354 ng.L-1, 24203 ng.L-1 in July, and 667 ng.L-1, 2526 ng.L-1 in October respectively. With the increasing migration distance of dissolved alkanes and dissolved fatty acids in underground river, their contents decreased. Based on the molecular characteristic indices of alkanes, like CPI, OEP, Paq and R, dissolved alkanes were mainly originated from microorganisms in July, and aquatic plants in October. Saturated straight-chain fatty acid had the highest contents in all samples with the dominant peak in C16:0, combined with the characteristics of carbon peak, algae or bacteria might be the dominant source of dissolved fatty acids.
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