Japanese eel larvae Anguilla japonica were collected in Jingjiang section of Yangtze River Estuary from January to April, 2012. The elements of sagittal otolith extracted from five larval eels were detected by using synchrotron radiation X ray fluorescence (SRXRF). Results showed that fourteen elements could be accurately detected. It included two major elements Ca and Sr, the average contens of which in otolith could reach 240 215.928 μg/g and 2 383.221 μg/g respectively. The other twelve were recognized as minor elements. Their contents sequentially decreased in the following order: Ba, Fe, Mn, Zn, Cr, Ni, Hg, Se, Co, Cu, Au, V. The average concentrations of Ba, Fe, Mn, Zn were 1-10 μg/g and the average concentrations of the other elements Cr, Ni, Hg, Se, Co, Cu, Au, V were less than 1 μg/g. According to spatial distribution and the content variation of all measured elements, Ca and Sr were the most stable elements whose coefficient of variation were 10.11% and 21.83%.By comparison, the coefficient of variation of Mn, Zn, Cr, Ni, Co varied from 23.11% to 35.88% and V, Hg, Au, Ba even exceeded 50%. The most unsteady element was Se for its coefficient of variation reached 134.31%. We also found that the variation of Sr/Ca ratios might be delayed in the otolith when Japanese eels larvae migrated from sea to freshwater.