To search useful fatty acid biomarkers in evaluating trophic relations or food web structure of complex rice paddy food webs, fatty acid compositions of a large number of aquatic invertebrates and vertebrates were investigated at rice paddy fields in Hong-Sung, South Korea. The studied paddy fields were managed under conventional practice, organic practice with winter flooding, and organic practice without winter flooding. In our study, 18:1ω9 content showed very strong relationship with δ15N signature, indicating that oleic acid would be a good biomarker for inferring trophic position. Also we found that three fatty acids appeared to be good biomarkers for food sources in organic rice paddy fields. α-linoleic acid (18:3ω3) contents were high in green plants such as green algae, vascular plants and chara species. 16:1ω7/16:0 appeared to be a good biomarker for diatoms. 18:1ω9 (oleic acid) contents appear to be a good biomarker for detrital sediment. Using these three identified biomarkers for food sources and stable isotope data, we summarize food webs in rice paddy field ecosystem.