The Yangtze River floodplain is critical for migratory waterbirds along the East Asian-Australasian Flyway (EAAF). Greater awareness of its global importance is urgently needed to ensure waterbird populations remain in favourable conservation status, as well as the enhancement of wider wetland biodiversity within this region. The designation of protected wetland areas and building a green ecological corridor in the Yangtze floodplain is now becoming a critical issue of interest to the Chinese government. Priority sites in this area were identified based on the criteria used to identify sites that qualify as Wetlands of International Importance (Ramsar Sites) and Important Bird and Biodiversity Areas (IBAs) by using multi-source data. The results show that 140 of the sites surveyed are priority sites. The Importance Index (I) for the whole floodplain decreased slightly from 2001-2005 and an unbalanced distribution pattern is evident with Jiangxi and Hunan provinces significantly higher than the other provinces in the floodplain. Although more than 60% of the priority sites are currently located outside protected areas, the average Conservation Effectiveness Index (C) of the whole floodplain is 75.6%, which suggests the coverage of protected areas for most wintering waterbird population is reasonable. Conservation of the Yangtze River floodplain needs to be further strengthened due to declining waterbird abundances and the mismatch between the distribution of protected areas and their importance for wintering waterbirds. A comprehensive system for priority site identification and protection and scientific review is needed. Multi-sourced data from regular, systematic and coordinated monitoring of waterbird distribution and abundance across the EAAF, as well as national scale citizen science programmes are also critically important.