Phosphorus (P) is an important macronutrient for all lives on earth, but it is also a finite resource. Therefore, it is important to understand how to increase the P availability and uptake. The endophytes can help host plants to improve P uptake and will be significantly affected by plant cultivars and genotypes. To investigate the mechanism of root endophytes in promoting the P uptake of peach rootstocks, we analyzed the variances of the root endophytic fungal and bacterial communities of peach rootstocks with different P efficiencies under high or low level of P addition.