The mineralization of organic P to orthophosphate in suspended particles by alkaline phosphatase plays an important role in phosphorus cycling in aquatic ecosystem, especially in shallow lake. The study on bacterial alkaline phosphatase-encoding genes is of great significance to reveal the microbial driving mechanisms of organic P mineralization. We identified the spatial and temporal distribution characteristics of the abundance of phoX and phoD genes in suspended particles in four ecological regions in Lake Taihu, a large shallow eutrophic lake,and explored the main environmental factors affecting the abundance of the two genes. The qPCR analysis suggested that phoD gene abundance was 6-42 times higher than phoX gene abundance in four ecological regions in the study period, and both of phoD and phoX genes abundance in suspended particles has significant difference in spatial and temporal distribution. The highest abundance of phoX (9.18×10⁴ copies/L) and phoD (1.88×10⁶ copies/L) were found in the river estuaries in June, followed by that in macrophyte-dominated zone, central lake zone and algae-dominated zone. Compared with the genes abundances in June, the abundance of phoD gene in four ecological regions decreased significantly in September while phoX gene abundance increased in algae-dominated zone and macrophyte-dominated zone. In September, the abundance of phoX gene (5.70×10⁴ copies/L) in macrophyte-dominated zone was the highest and the lowest was in the river estuaries (1.49×10⁴ copies/L). Macrophytes play an important role in determining the abundance of phoD and phoX genes. The abundance of phoX genes in suspended particles may be underestimated. Dissolved oxygen, total nitrogen and total phosphorus are the main environmental factors affecting the abundance of bacterial phoX and phoD genes in suspended particulates.