The genetic diversity of 15 Caragana populations (7 Caragana microphylla populations and 8 Caragana intermedia populations) from east to west at Inner Mongolia Plateau was analyzed by ISSR (intersimple sequence repeats) markers.The results showed that the percentage of polymorphic loci of 7 C.microphylla populations was 98.19%;Nei’s gene index and Shannon information index were 0.289 7 and 0.444 0,respectively;the genetic differentiation coefficient(G_st) was 0.119 0,which showed that there is a moderate genetic differentiation in C.microphylla populations;and the gene flow(N_m) among populations was frequently(3.701 0).(2)The percentage of polymorphic loci of 8 populations of C.intermedia was 99.7%,Nei’s gene index was 0.312 8,Shannon information index was 0.478 4;the genetic differentiation coefficient(G_st) was 0.188 1,which showed that C.intermedia population have great genetic differentiation;the gene flow (N_m) was 2.157 8.(3)Genetic diversity and genetic differentiation of C.intermedia both higher than that of C.microphylla,which is genetics base that C.intermedia instead of C.microphylla to adapt to adverse environmental and extended distribution.(4)Neighbor cluster analysis showed that 15 Caragana populations is gradually from east to west,which reflected both in the gradual change of geography distribution and geographic alternative.Correlation analysis of genetic diversity index and meteorological factors and soil factors showed that the average temperature plays an important role in Caragana populations genetic differentiation.