Abstract: In this study, six single-copy nuclear gene markers were used to study the nucleotide polymorphisms and genetic structures of 14 natural populations of Populus davidiana Dode. Results showed that P. davidiana harbored high levels of nucleotide polymorphisms. The average gene flow (N_m) among populations was 0.66; the percentage of variation within the population (71.82%) was greater than that among populations (28.18%). The Mantel test illustrated that there was no correlation between geographical and genetic distances. Results of mismatch distribution demonstrated that P. davidiana experienced historical population expansion. The comprehensive population history, high outcrossing, and high rate of base mutations were the main factors contributing to the high level of nucleotide polymorphisms. The high dispersal of pollen and seeds as well as continuous distribution resulted in the relatively low genetic differentiation.