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Purpose: Phosphorus (P) is the main factor limiting crop production in red soils. Examining the bacterial community harboring phoD gene under different long-term cropping systems may supply meaningful insights for improving soil P availability. Here, we analyzed how the cropping systems affect community structure of phoD-harboring bacteria by changing physicochemical properties in red soils. Materials and methods: Twenty-four soil samples from eight cropping systems (abandoned farmland, corn continuous cropping, mango continuous cropping, taro continuous cropping, zucchini–corn rotation, pea–corn rotation, canola–tobacco rotation, and walnut–tobacco intercropping for > 10 years) were collected from 0 to 20 cm depth in Miyi County, Sichuan Province, China. The abundance of phoD gene was determined by quantitative PCR, and phoD-harboring bacterial community structure was analyzed by high-throughput sequencing. Results and discussion: Available P concentration and phoD abundance were the highest in pea-corn rotation soil, while alkaline phosphatase (ALP) activity was the lowest in this soil. Available P showed a significant positive relationship with phoD abundance, while a negative relationship with ALP activity. Moreover, the dominant phyla of phoD-harboring bacterial community were Proteobacteria and Actinobacteria, with Cupriavidus and Bradyrhizobium being the dominant genera. The relative abundances of Streptomyces, Pseudomonas, and Amycolatopsis were positively related to soil P concentration (total and available P) and negatively related to ALP activity, indicating that these genera may be essential in the mineralization of soil organic P. Redundancy analysis (RDA) showed that ALP, soil organic carbon (SOC), and N:P ratio were the remarkable factors affecting the structure of phoD-containing bacterial community across all cropping system soils. Meanwhile, structural equation model (SEM) showed that the effects of total N and available P on soil phoD-harboring bacterial community structure were stronger than that of SOC. Further, soil texture was also one of the main factors affecting the phoD-harboring bacterial community structure, which had a notable up-regulation effect on abundance and diversity of phoD gene and indirectly regulate gene composition by affecting available P. Conclusions: The long-term cropping systems can affect the community structure of phoD-containing bacteria and ALP activity by altering physicochemical properties, and thus contribute to regulation of the biogeochemical cycle of P in red soils. The main factors driving the changes in phoD-harboring bacterial community structure were soil texture, SOC, total N, and available P. [ABSTRACT FROM AUTHOR]