At present, the resources of anadromous fish in the world are drastically reduced and one of the solutions to promote its recovery may be to identify and protect its feeding grounds. To determine whether the feeding grounds of anadromous Coilia nasus in the Yangtze River are still in the sea area, the quantitative line analysis of Sr and Ca contents (Sr/Ca ratios) and the area distribution analysis of Sr content in the otoliths of C. nasus in three water areas (Poyang Lake, Yangtze River estuary and Shengsi Sea area) were carried out by electron probe microanalysis (EPMA) to analyze the habitat use and the migratory patterns of different estuarine C. nasus. These results showed that the Sr/Ca ratios of all otoliths fluctuated significantly. By comparison, it was found that C. nasus of Yangtze River might exist in the Shengsi Sea area, and the Shengsi Sea area might be one of the feeding grounds of migratory C. nasus. Therefore, it is urgent to carry out a comprehensive investigation on the distribution of related groups in the Shengsi Sea area and the influence of potential threat factors, such as fishing and harsh habitat, to effectively protect the resources and habitats of C. nasus in the Shengsi Sea area.

In the protection of migratory species, Coilia nasus has always been a research topic of very high interest in various countries because of the high economic value and the serious decline of resources. In this study, C. nasus were collected from the Shengsi Sea area, the Yangtze River estuary, the Taizhou section of the Yangtze River and Poyang Lake. By using 2b-RAD simplified genome sequencing technology, 63,110 SNP sites were screened, and the genetic diversity of each population was analyzed with SNP markers. The results showed that (1) the genetic purity of the four groups of populations was not high, with the need to further increase levels of genetic purity; (2) the genetic diversity in the four populations was high, indicating that they had strong adaptability to environmental changes and could easily expand their distribution and resource growth; (3) the F_ST values (0.112–0.142) of the four populations were higher, indicating that there was moderate genetic differentiation, but no independent population was formed. This study speculated that these migratory species may have the same spawning grounds and pointed out that the gene purity of C. nasus may have been polluted, and it is urgent to improve the purity in the protection of migratory C. nasus.