Knowledge of taxonomic diversity is critical to understanding the taxonomic relatedness of species and unevenness of taxonomic structure. We evaluated the temporal and spatial variation in taxonomic diversity of fishes in Haizhou Bay, China using data collected from five comprehensive surveys of the bay between March–December, 2011. We used a generalized additive model (GAM) to analyze the relationship between taxonomic diversity of fishes and environmental factors. We identified 96 fish species in HaizhouBay, belonging to 2 classes, 13 orders, 44 families, and 71 genera. The average taxonomic distinctness () was 79.5 and the variation in taxonomic distinctness () was 200.6. Both these taxonomic diversity indices exhibited seasonal and spatial variation related to the seasonal migration of fishes and changes in the environment. Water depth and benthic levels of dissolved oxygen had a significant effect on the of fishes. Similarly, water depth, benthic levels of dissolved oxygen, benthic water temperature, and month were the most important environmental factors influencing the of fishes in Haizhou Bay. The two taxonomic diversity indices decreased along a line from north to south, suggesting that latitude has an important influence on the spatial distribution of taxonomic diversity in fishes.