Abstract: In order to explore the spatial distribution patterns of the phylogenetic diversity of fish community and the maintenance mechanism in the Yellow River Estuary and its adjacent waters. The phylogenetic α and β diversity and their relationship with different influencing factors were examined considering phylogeny of fish species based on data collected from the surveys in June, July, August and October in 2013 and February, April and May in 2014. The results showed there were significant monthly variations in the phylogenetic α diversity of fish community. The PSV and PSR were significantly lower in February, April, and May, and PSE was significantly higher in April and May. Sea surface temperature (SST) and sea surface salinity (SSS) significantly influenced the phylogenetic α diversity. Phylogenetic β diversity were relatively high across different months and different stations regardless of whether the multi-site dissimilarity or the pairwise dissimilarity calculation methods were used, the turnover component drove the changes in phylogenetic β diversity. Sea surface salinity and spatial distance had significant impacts on phylogenetic β diversity and turnover components. The α and β diversity exhibit noticeable spatio-temporal variations, and environmental factors and spatial distance are the primary factors influencing the changes in phylogenetic diversity of fish community in the Yellow River Estuary and its adjacent waters.