Abstract: Coilia nasus is a valuable fish in the middle and lower reaches of the Yangtze River. In order to reconstruct its habitat history, an electronic probe microanalyzer (EPMA) was applied to analyze the microchemistry patterns of element Sr and Ca in otoliths of 17 individuals of two phenotypes belonging to short-jaw C. nasus (once named as C. brachygnathus) and long-jaw C. nasus. Au sample were collected in Hexian section of the Yangtze River in Anhui Province at May 2015. Microchemical results showed that C. brachygnathus individuals could be divided into two types: (1) Sr/Ca ratio was consistently at low phase (<3.0) throughout the otolith, indicating that the individuals only experienced freshwater habitat during their whole life history; (2) Sr/Ca ratio fluctuated between low (2.39±1.18—2.63±0.85) and high (3.22±1.17—3.29±1.14) phases in the otoliths, suggesting the individuals experienced not only freshwater, but also brackish water habitats at different stages in their life history. The otolith Sr/Ca ratio of long-jaw C. nasus fluctuated significantly between low (<3, reflecting freshwater habitat) and high (>3, reflecting estuarine brackish water or sea water habitat) value phases. The 16- color-Sr concentration profiles are in the line with the srlca ratios. All of the above results revealed that the resource composition of Coilia nasus from Hexian section of the Yangtze River in Anhui Province was much more complex by consisting of freshwater resident and fresh-brackish water migratory short-jaw C. nasus, as well as anadromous long-jaw C. nasus individuals.