Caragana microphylla, C. davazamcii and C. korshinskii exhibit a geographical replacement series from east to west in the Inner Mongolia Plateau. Currently there is still a debate about the taxonomic and genetic relationship among these 3 species. We studied the genetic diversity and the genetic relationship among these 3 species by analyzing individual plant DNA samples from within 10 populations with RAPD markers. We identified 678 RAPD loci in total, of which all were polymorphic (PPB=100%). There were 41 unique loci (6.05％). In general, a trend presented that the genetic diversity of these species decreases from east to west. Further, the genetic diversity negatively correlated with the local annual mean temperature significantly. AMOVA showed that the genetic variation among these 3 species was only 6.08％ of the total genetic variation. Between the species, the genetic variation was insignificant (P＝0.9961). The proportion of genetic variation among populations within each species was 11.90％(P<0.001), and the genetic variation existed mainly within the populations(82.02％). The genetic differentiation within the populations, estimated with Shannon’s index (Hpop/Hsp), was 0.8013; the coefficient of gene differentiation (Gst) was 0.1603; and the Nm was 2.6192. This thus indicates that there is relatively high gene flow among these populations which suggests that these 3 species are crossbreeding. The genetic diversity level and the population distribution pattern showed geographic continuity to some extent.