Ten cpSSR markers were used to detected genetic diversity and relationship among fourteen species of Caragana. The genetic diversity was 0.860 to 2.138, with an average of 1.258. The effective number of alleles for each cpSSR locus ranged from 2.051to 7.407, with an average of 3.530.Ten cpSSR primers detected totally 92 polymorphic loci, the value of allelic polymorphism information content (PIC) ranged from 0.512 to 0.865, on an average, 0.671 per primer. The value of genetic similarity (GS) indexes among fourteen species of Caragana varied from 0.51 to 0.93, on an average of 0.77. These indicated that the genetic diversity at the genomic level of the selected source germplasm was rich, and was representative of the diversity of the germplasms, in general. Cluster analysis showed that fourteen Species of Caragana tested in this study could be clustered into four groups, cpSSR analyzed inter-genetic relationship was almost consistent with traditional morphologic result.