Abstract: Community assembly mechanisms and species coexistence have long been central in ecological studies. Up to now, 3 mechanisms of community assembly have been proposed: neutral assembly, competitive exclusion and habitat filtering. Neutral mechanism emphasizes that all species in a community are equivalent ecologically, and the species composition in communities are determined by their random processes and dispersal limitation. Competition exclusion holds that species with similar or overlapping niches cannot coexist stably for a long time, because strong interactions among species would result in niche differentiation, leading to the species constituting a community showing character differentiation. Habitat filtering holds that the local environmental conditions are usually very special, which make only the species adapted to the environment can exist. In recent years, the analysis of phylogenetic community structure provides a new and useful method for exploring mechanisms of community assembly. The Poyang Lake is the largest freshwater lake in China, and one of the 3 only lakes which still have natural connection to main stream of the Yangtze River. Therefore, investigation of fish community assembly mechanisms in the Poyang Lake is of great significance to understanding origin and maintenance of the biodiversity in the Yangtze River basin. In the present study, we selected 24 sites to collect fish samples in Poyang Lake and its tributary, the Xiushui River, between July and September 2018. Fishes were collected by various methods, including fishing and market survey. Specimens were fixed in 10% formalin and transferred to 75% ethanol for final preservation. All specimens were identified to species by morphological and molecular systematic characters. Cluster analysis was carried out to explore community structure according to the presence-absence data of fish species in each sampling site. Combining the results of cluster analysis and fish spatial distribution for each sampling site, the fish communities in Poyang Lake were classified to identify subgroups. Genomic DNA was extracted from muscle samples using the high salt method. Universal primers L14724/H15915 and some specific primers were used to amplify and sequence cyt b gene through polymerase chain reaction. According to the 900 bp segment corresponding to the cyt b gene, the genetic distance among species was calculated by MEGA X. Phylogenetic community structures of fish species in different sampling sites and regions were analyzed based on the genetic distance and presence-absence data of fish species in each sampling site by the package picante in R, to explore the fish community assembly mechanism at different spatial scales. A total of 106 species were collected during the study period, which belonged to 8 orders, 15 families and 60 genera. Among them, Clupeiformes comprised 2 species; Cypriniformes 72 species; Siluriformes 18 species; Beloniformes 1 species; Synbranchiformes 2 species; Gobiiformes 4 species; Anabantiformes 2 species; Perciformes 2 species. Among the 60 species, Cyprinidae is the main group, accounting for 56.6% of the total species. These species showed the compositional characteristics of river-lake fish fauna of East Asian region. A total of 86 fish species were collected in the lake area, which showed a decrease in species richness compared with several surveys of fish resources in the Poyang Lake in the past 60 years. However, compared with the 72 species recorded in the survey in 2010, the species richness of fish in the Poyang Lake was increasing. According to the species composition and spatial distribution, the fish communities of the Poyang Lake Basin can be divided into the Poyang group and the Xiushui group. The fish communities of the Poyang group can be further divided into three sub-groups: the Northern group, the Southern group and the Eastern group. In the analysis of phylogenetic community structure, the fish communities of 12 survey sites were driven by habitat filtering at the local scale, where the sampling sites were close to the tributary estuary and with special environmental conditions; while the fish communities in the other 12 sites were driven by competition, because they contained more far-related species. At the regional scale, the fish communities of the Northern group, the Eastern group and the Xiushui group were structured by competitive exclusion, while fish communities of the Southern group were structured by environmental filtering. At the scale between lake and tributary, the fish communities of the Poyang Lake group were structured by competitive exclusion, while fish communities of the Xiushui group structured by environment filtering. In the present study, species composition and community assembly mechanisms of the fish communities of the Northern group, the Southern group, the Eastern group and the Xiushui group were different, indicating that the fish communities in different regions of the Poyang Lake were affected by different factors. In overall, the different assembly mechanisms of fish communities revealed by the present study showed that community species composition was shaped by both environmental factors and spatial scale. We believe that our results will be useful for understanding of community assembly mechanisms and may provide a theoretical basis for fish conservation in the Poyang Lake Basin.