The object of this work was to explore the intrinsic factors of phenotypic differentiation among natural populations of Styrax dasyanthus Perkins. The genetic diversity of 6 natural populations of S. dasyanthus was analyzed by 14 phenotypic traits and microsatellite markers. The results showed that:（1） there was significant differentiation in 14 phenotypic traits among populations and within population. The mean phenotypic differentiation coefficient (V_st) was 22.64%, and the phenotypic variation of populations of S. dasyanthus within population was higher than that among populations, which indicated that the phenotypic variation mainly from variance within population. （2） a total of 43 alleles were identified in 87 individuals by 4 microsatellite primers, with a mean value of 10.63 alleles per primer and the average percentage of polymorphic loci (P) was 100%. The mean observed heterozygosity (H_o) and expected heterozygosity (H_e), Shannons information index (I) were 0.659, 0.811, 1.894, respectively. The genetic diversity within population (H_s) was up to 0.811, and the genetic diversity among populations (D_st) was only 0.110. The genetic differentiation coefficient (F_st) among populations was 0.118, indicating that the percentage variation among populations was 11.8%, and the percentage variation within population was 88.2%, which was consistent with the conclusion of phenotypic variation research roughly. The test results of phenotypic traits and microsatellite markers showed that there was abundant genetic variation in the natural population of S. dasyanthus, and the higher genetic flow (N_m=2.050) allowed the genetic variation among populations to be less than that within population.