The genetic diversity of Agropyron mongolicum from six natural populations and two cultivars in the central and east regions of Inner Mongolia was synthetically assessed. It was showed that A. mongolicum possessed a higher genetic diversity within population than that among populations as a result of the cross-pollinated breeding system. Between natural populations and cultivars, the genetic diversity among six natural populations was much higher than that between two cultivars, owing to the environmental heterogeneity of natural populations. In the meantime, there also was a genetic differentiation between two cultivars. It was clear that artificial selection played an important role in the differentiation. UPGMA cluster analysis showed that eight populations could basically be divided into three groups adapting to their own soil conditions. These groups were sand-land populations, gravelly-slope populations and sandy soil cultivars respectively. It is enough to prove that natural and artificial selections have an enormous effect on the differentiation among populations.