Abstract: Guangdong has the longest coastline of all provinces in China, with many coastal wetland types. However, long term waterbird observation, which is crucial for wetland conservation, has only been carried out in a few sites. To understand the wetland bird diversity patterns of the Guangdong coast, identify the main ecological environment problems and assess the ecosystem stability, surveys were conducted every winter between 2016-2019 at Leizhou Bay and Shantou coastal wetlands. Species-level, functional and phylogenetic diversities were analyzed separately. After three years of observation, a total of 96 048 waterbird individuals belonging to 63 species, 10 families and 6 orders were recorded. Among them, the wintering waterbirds in Shantou consisted of members of the Charadriiformes, Anseriformes and Ciconiiformes, while members of the Charadriiformes dominated in Leizhou Bay. There was no significant difference in species diversity between the two sites. Though, no significant difference was observed in functional evenness of traits for body mass, feeding guild and foraging location, functional divergence of these traits were significantly higher in Shantou than in Leizhou Bay. Two phylogenetic diversity indices including mean pairwise distance and mean nearest taxon distance all shown significant difference between the two sites. The results of the phylogenetic diversity analysis show the waterbird assemblages in Leizhou Bay were mainly structured by environmental filtering, which were phylogenetically clustered (SES.MPD < 0). In contrast, asemblages in Shantou were phylogenetically overdispersed (SES.MPD>0), showing some interspecific competition in this area. The result indicates that the differences of functional traits and phylogenetic structures were driven by local geographical location, habitat composition, human disturbance and other environmental factors. Corresponding protection measures and ecological restoration strategies should be developed according to the characteristics of the respective waterbird assemblages.