Huagaimu (Manglietiastrum sinicum) trees are critically endangered species and classified as a plant species with extremely small populations in China. Rhizospheres and bulk soils prokaryotic communities play an important role to protect and promote plants health and growth. However, the compositions and structures of prokaryotic communities in wild and reintroduced M. sinicum rhizospheres and bulk soils are still poorly understood. In the present study, prokaryotic communities in wild and reintroduced M. sinicum rhizospheres and bulk soils were compared using high-throughput sequencing. Thirty-two phyla, 76 classes, 193 orders, 296 families, and 470 genera of prokaryotes were obtained. Proteobacteria and Acidobacteria were the two most abundant phyla in all soil samples. The compositions and structures of prokaryotic communities were overall similar, and the abundance of some taxa varied significantly among soil samples. Soil prokaryotic communities were significantly affected by soil pH, total nitrogen, total phosphorus, and total potassium. Eleven of predicted functions were significantly different among the four soil groups. This study provides for the first insights into the compositions, structures, and potential functions of prokaryotic communities associated with wild and reintroduced M. sinicum rhizospheres and bulk soils, and providing a foundation for future research to help protect this endangered species.