Abstract:Genetic differentiation of four Stipa krylovii populations collected from meadow steppe, typical steppe and desert steppe in middle and eastern Inner Mongolia steppe, was studied with a combination of morphological and RAPD markers. (1) Neither Euclidean’s distance matrix based on morphological data nor Nei’s unbiased genetic distance matrix had any significant relationships with geographic distance matrix in the region. This indicated that genetic differentiation of Stipa krylovii populations was affected mainly by natural selection. (2) One way ANOVA and AMOVA showed that there were significant morphological divergence and genetic differentiation. (3) The relationship was not significant between Euclidean’s distance and Nei’s unbiased genetic distance by Mantel test, suggesting that the evolutionary force was not identical on morphological divergence and genetic differentiation.