Leymus chinensis (Trin.) Tzvel is the characteristic of the Eastern Asia, and is a perennial herbaceous rhizome species on L. chinensis steppe of the Northern China, the Eastern Mongolia, and area of Outer-Baikal of Russia. It has both vegetative and sexual reproductions, and results in complexity of the population structure. Thus, it is difficult to identify distinct clones. Author used the randomly amplified polymorphic DNA (RAPD) technique to identify the clonal structure of heterogeneous and homogeneous habitats in two populations ofLeymus chinensis, analyzed 260 ramets samples using 12 primers and 60 polymorphie markers (reproducible RAPD bands). The results proved elonal diversity described using PD, D, and E was higher in the HCS habitat than that in the HPS habitat. The PD, D, and E in the HCS of Songzhan population were 0.21, 0.90, and 0.91, respectively, whereas the PD, D, and E in the HPS of Songzhan population were only 0.09, 0.68, and 0.77, respectively; the PD, D, and E in the HCS of Yongle population were 0.19, 0.92 mad 0.90, respectively, correspondingly, these measures in the HPS of Yongle population were only 0.09, 0.63, and 0.79, respectively. The results also indicated that clonal population ofL. chinensis in HPS habitat had lower genetic dissimilarity index than that in the HCS habitat.