In order to reveal the variation degree and variation patterns of the phenotypic in Michelia yunnanensis,we investigated 14 phenotypic traits for 180 individuals in 6 natural populations of M.yunnanensis from Kunming City in Yunnan Province of China and used nested analysis,correlation analysis,variance analysis,Shannon-Weaver diversity index and cluster analysis to analyze results.The results showed that:(1)There were significant differences in the phenotypic variation among and within populations.Phenotypic differentiation coefficient (VST) among populations (24.38%),was less than that of within populations (75.62%).The variation within-populations comprised a majority of total phenotypic variation.Coefficient of variation (CV) varied from 16.20% to 60.11% showing the high variation of the phenotypic traits.(2)The Shannon-Weaver index analysis shows that there were rich diversity in M.yunnanensis various populations and the total mean diversity index was 1.772.(3)According to the UPGMA cluster analysis,the po-pulations of M.yunnanensis in this study could be divided into three groups.These cluster results were not due to geographic distances.Utilizing of variation within and among populations is important significance for genetic improvement of M.yunnanensis.