Background: Han River estuary is a national wetland reserve near the Demilitarized Zone (DMZ) between South Korea and North Korea. This trans-boundary estuary area has been well preserved and shows distinctive plant communities along the salinity gradient. To elucidate energy flows and nutrient cycling in this area, we studied trophic relations between the dominant sesarmid crab, Sesarma dehaani, and food sources in three wetlands with different environments along the estuarine gradients. Results: Stable isotope signatures (δ 13 C and δ 15 N) of the crabs were significantly different among the sites and body size classes. Seasonal changes in δ 13 C of small crabs were distinct from those of large individuals at all the sites. The isotopic values and fatty acid profiles of the crabs were more different among the sites in September than in May. In May, large-sized crabs utilized more plant materials compared to other dietary sources in contrast to small-sized crabs as revealed by a stable isotope mixing modeling, whereas contributions to diets of crabs were not dominated by a specific diet for different body size in September except at site 1. Based on PCA loadings, fatty acid content of 18:3ω3, known as a biomarker of plant materials, was the main factor to separate size groups of crabs in May and September. The δ 13 C value of sediment had high correlation with those of small-sized crabs at site 1 and 2 when 1-month time lag was applied to the value for crabs during the surveyed period. Conclusions: Based on the stable isotope and fatty acid results, the consumption habits of S. dehaani appear to be distinguished by sites and their size. In particular, smaller size of S. dehaani appears to be more dependent on fewer food sources and is influenced more by the diet sources from the sediments in Han River estuary.