Morphological and AFLP-based genetic analyses of six natural populations of Rosa platyacantha in the Eastern Tianshan Mountains of Xinjiang in Northwestern China were performed. Nested analysis of variance models(ANOVA) showed that there were significan differences(P > 0.05)in morphological traits among and within the populations of R. platyacantha. The phenotypic variation coefficien(CV) of the traits varied from9.78% to 37.71%, confi ming the abundant phenotypic variations in the species. The average value of the phenotypic differentiation coefficien(Vst) was 27.50%, indicating a lower phenotypic diversity among populations than within populations. Principal component analysis(PCA) showed that the two decisive traits of ANH and TAW contributed to the proportion of 97.19% in the 1st principal component(PC), suggesting that the phenotypic variations of the traits primarily originated from the achene characters. The percentages of polymorphic loci(PPL), Nei’s genetic diversity index(h) and Shannon information index(I) were highly similar among populations, with average values of 63.96%, 0.2361 and 0.3506,respectively. Moreover, the gene differentiation(Gst) and estimated value of gene fl w(Nm) were 8.10% and 5.6766, respectively, indicating very low genetic diversity among populations. Clustering analysis based on morphological traits and AFLP markers showed that the populations were mainly grouped with similar altitudes and geographic distances, respectively. The Mantel test revealed that there was no significan correlation between the phenotypic and genetic diversity among populations, implying a possible influenc of environments on the genotypes of R. platyacantha. Morphological and AFLP-based genetic analyzes of six natural populations of Rosa platyacantha in the Eastern Tianshan Mountains of Xinjiang in Northwestern China were performed. Nested analysis of variance models (ANOVA) showed that there were significant differences (P> 0.05) in morphological traits among and within the populations of R. platyacantha. The phenotypic variation coefficien (CV) of the traits varied from 9.78% to 37.71% confi ming the abundant phenotypic variations in the species. The average value of the phenotypic differentiation coefficien (Vst) was 27.50%, indicating a lower phenotypic diversity among populations than within populations. Principal component analysis (PCA) showed that the two decisive traits of ANH and TAW contribute to the proportion of 97.19% in the 1st principal component (PC), suggesting that the phenotypic variations of the traits primarily originated from the achene characters. The percentages of polymorphic loci (PPL), Nei’s genetic diversity index (h) and Shannon information index (I) were most similar among populations, with the average values ​​of 63.96%, 0.2361 and 0.3506, respectively. The gene differentiation (Gst) and estimated value of gene fl w (Nm) were 8.10% and 5.6766, respectively, indicating very low genetic diversity among populations. Clustering analysis based on morphological traits and AFLP markers showed that the populations were mainly grouped with similar altitudes and geographic distances, respectively. The Mantel test revealed that there was no significan correlation between the phenotypic and genetic diversity among populations, implying a possible influenc of environments on the genotypes of R. platyacantha.