The nrDNA internal transcribed spacer (ITS) and cpDNA trnL-F internal spacer (IGS)sequence data of Caragana eight species and one outgroup Halimodendron halodendron, was employed to reconstruct a phylogenetic tree, then the area relationship was analyzed by means of component analysis (CA), Brooks parsimony analysis (BPA), and dispersal-vicariance analysis (DIVA), six areas were selected from two divided distributions of East Asia and Tethys in Caragana.The phylogenetic tree indicated that there were three distinctive groups, which were attributed to some morphological characters, first with pinnate foliage and deciduous rachis, second with palmate foliage and persistent sclerotic stick rachis, and third with pinnate foliage and persistent sclerotic stick rachis. The results of CA and BPA illustrated general area relationships. An explicit area relationship should be Altai-Sayan, Far East-NE China and North China (Hengduan Mountains). DIVA recognized several explanatory vicariance and dispersal events. As the scenario of Caragana distribution pattern, it looks like the vicariance versus dispersal plays more important role. In vicaraince, there are not only the isolated far-distance vicariance, but also the adjacent vicariance especially a vicariance between Hengduan Mountains and North China.