In order to reveal the phenotypic diversity and variation pattern of Alpine Rhododendron species, we measured 12 phenotypic traits of Rhododendron rubiginosum natural populations at five different altitudes in Jiaozi Mountain National Natural Reserve of Yunnan Province and studied the levels of phenotypic diversity by using ANOVA analysis, correlation analysis and cluster analysis. The results indicated that: (1) there were significant differences in phenotypic variations among and within populations. Coefficient of variation (CV) of these traits ranged from 8.51% to 34.32%, and RHL (R′) ranged from 38.04% to 100%. High phenotypic variations were occurred in the relative low elevation populations (P1 and P2), while low degree of variations occurred in the moderate and high elevation populations (P3、P4 and P5). (2) Based on the ShannonWeaver diversity index (H′) analysis, the mean phenotypic diversities index of 5 sample elevation populations was 2.453 4, and the mean phenotypic diversity index of 12 phenotypic traits was 4.076 3. It indicated that there were richness phenotypic diversity in R. rubiginosum populations. (3) The correlation analysis showed that there were significant correlations among these traits. There were significant negative correlations between elevation and FSL and IW. However, there was no significant correlation between elevation and other traits. (4)The 5 sampled populations of R. rubiginosum could be divided into two groups according to the UPGMA cluster analysis. Therefore, the trait variations of natural populations at different altitudes were affected mainly by microenvironmental heterogeneity of different R. rubiginosum populations.