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Background:Parasites have adverse effects on the life and survival of many migratory waterbirds, especially birds on the endangered species list. Hooded Cranes are large migratory colonial waterbirds wintering in wetlands, which are prone to parasite infection, thus monitoring the diversity of parasites is important for sound wetland management and protection of this species. Methods:From November 2012 to April 2013, we collected 821 fresh faecal samples from the three lakes (Poyang, Caizi and Shengjin Lake) in the lower and middle Yangtze River floodplain, and detected with saturated brine floating and centrifugal sedimentation methods. Parasite eggs were quantified with a modified McMaster’s counting method. Results:In this study, 11 species of parasites were discovered, i.e., two coccidium (Eimeria gruis, E. reichenowi), five nematodes (Capil aria sp., Strongyloides sp., Ascaridia sp., Trichostrongylus sp., Ancylostomatidae), three trematodes (Echinostoma sp., Echinochasmus sp., Fasciolopsis sp.) and one cestode (Hymenolepis sp.). About 57.7%of the faecal samples showed parasitic infection. All species of parasites were found at the three sites except Hymenolepis which was not found at Poyang Lake. While most samples were affected by only one or two species of parasites, infection by Eimeria spp. was the most common (53.1%). From One-Way ANOVA analysis of the three lakes, parasite species richness index (p = 0.656), diversity index (p = 0.598) and evenness index (p = 0.612) showed no significant difference. According to the statistical analysis of our data, there were no significant difference in parasite species richness index (p = 0.678) and evenness index (p= 0.238) between wintering periods, but a strong difference in diversity index (p < 0.05). Conclusions:Our study suggests that in the wintering Hooded Crane populations, parasite diversity is more sensitive to changes in the overwintering periods than to locations. This also indicates that with the limitations of migration distance, the parasites may not form the differentiation in Hooded Crane populations of the three lakes.