The genetic diversity of Magnolia sieboldii was assessed with simple sequence repeat (SSR, also known as microsatellite) DNA marker technique among 9 populations in seven provinces of China. The results indicated that: (1) A lower genetic diversity of 0.098 5 for the average Nei gene diversity (H), 0.146 8 for the average Shannon information index (I), and 0.597 9 for gene flow（＜1, again relatively low）among the 9 populations. (2) Certain genetic differentiation has occurred over longterm evolution, with genetic distance ranging from 0.068 8 to 0.214 2 and genetic similarity from 0.82 to 0.93. (3) The clustering analysis suggested that the 9 populations have evolved into two main branches, one with the Majiang population in Guizhou Province and the other with the rest of the populations. Comparatively, the Majiang population was in poor conditions. (4) The genetic diversity of M. sieboldii was positively related to population longitude. Our results suggest that the low genetic diversity and gene flow among M. sieboldii populations are probably the main genetic mechanisms of the species becoming endangered.