The estuarine tapertail anchovy Coilia nasus is a highly valued fish in the Yangtze River, however, its resources have drastically declined due to anthropogenic impacts, e.g., overfishing, habitat degradation, water pollution. This small anchovy has been recently proposed for listing as a Class Ⅱ protected species by the plan for adjustment on China's List of Wildlife under Special State Protection. The long-jaw(supermaxilla) estuarine tapertail anchovy is believed to be an anadromous ecotype of C. nasus with a length ratio of upperjaw to head>1. Anadromous C. nasus has much higher commercial value than that of another freshwater residen tecotype of this species with a length ratio of upper jaw to head<1. In order to understand the migration characteristics of the long-jaw C. nasus, an electronic probe microanalyzer(EPMA) was applied to analyze the microchemistry patterns of element Sr and Ca in otoliths of ten C. nasus of this ecotype collected form Nanjing section of the Yangtze River in 2009 and 2014. The results of line transect analyses showed that the Sr:Ca ratio(i.e., Sr/Ca×10³) in the otolith of the anchovies could be divided into two patterns: ① Sr/Ca ratio fluctuated between low(<3.0) and high(>3.0) phases in the otolith, suggesting the individuals were typical anadromous ecotype which experienced not only the freshwater, but also the brackish water, even the sea water habitats at different stages in their life history. ② Sr/Ca ratio was consistently at low phase(<3.0) throughout the otolith, indicating that the individuals only experienced freshwater habitat during its whole life history. These evidences were supported by the Sr mapping analyses of EPMA. The results showed, for the first time, that the habitat use of long-jaw grenadier anchovy was much more flexible, and furthermore, freshwater resident individual could even be found in long-jaw grenadier anchovies, although it is traditionally believed that every individual of long-jaw C. nasus in the Yangtze River is diadromous ecotype. Therefore, anadromous and freshwater resident C. nasus cannot be effectively distinguished only by the length ratio of upper jaw to head. However, otolith microchemistry analysis can provide an objective approach to solve successfully this problem of C. nasus fishery management.