Three ecotypes of Coilia nasus were identified: the anadromous stock migrated between the Yangtze River and sea, the freshwater stock resided in the Yangtze River and its adjoining lakes, and the landlocked stock in lakes isolated to the Yangtze River. In order to find parasite indicator to separate the three stocks of C. nasus, species composition and diversity of helminth communities were investigated. A total of 10 species of helminths were found in 407 C. nasus from the 9 sampling localities: 3 of monogeneans, Heteromazocraes lingmueni, Helciferus tenuis and Sinomazocraes changjiangensis in the gills; 1 of digenean Elytrophallus coiliae in the stomach; 3 of nematodes, Anisakis simplex, Contracaecum sp. and Eustrongylides sp. in the intestine; 3 of acanthocephalans, Acanthosentis cheni, Arhythmacanthus parasiluri and Brentisentis yangtzensis in the intestine and the pyloric caeca. H. lingmueni and A. cheni with rather high prevalence and mean abundance were found in the 3 ecotypes of C. nasus. The marine helminths, such as H. tenuis, Contracaecum sp. , and E. coiliae were only found in the anadromous stock, which suggested that the 3 helminths can be used as biological tags for discrimination of the anadromous stock. The freshwater helminths, such as S. changjiangensis, A. parasiluri and B. yangtzensis, with low infection levels were only found in the freshwater stock, which suggested that the 3 parasites can be used as indicator for the freshwater stock. Mean species richness and the Brillouin diversity index were highest in helminth community in the anadromous stock, higher than 1.25 and 0.19, respectively. Species richness and diversity in the other two stocks were lower than 0.79 and 1.12, respectively. The low diversity in helminth communities of freshwater and landlocked stocks was due to the low infection levels of freshwater parasites and the loss of marine helminths, which was probably caused by the salinity decrease and the absence of the intermediate hosts of marine helminths in freshwater habitat. In addition, geographical isolation could also prevent exchanging of the anchovy and helminths and then lead to decrease of diversity in the landlocked stock.