The taxonomic treatment of Caragana davazamcii Sancz. has been a controversial matter, as its relationship with C. microphylla Lam. and C. korshinskii Kom. is not clear. It was treated as an independent species, or a variety under C. microphylla or C. korshinskii. This study is to examine the interspecific relationship of these three species and the origin of C. davazamcii based on internal transcribed spacer (ITS) and non-coding region of chloroplast trnL-F, combined with morphological data and geographical distribution. The trnL-F sequence of C. davazamcii is identical to that of C. microphylla but differs distinctly from that of C. korshinskii. The high congruence of ITS copies through both direct and cloning sequencing rejects the recent hybridization hypothesis of C. davazamcii between C. microphylla and C. korshinskii. In contrast, two different ITS sequence copies were found respectively in each individual of C. microphylla and C. korshinskii. One of the two ITS sequences in C. microphylla is identical to that of C. davazamcii. This result indicates that C. davazamcii might have taken part in the hybridization of C. microphylla as one parent , or that extensive gene flow might have occurred between these two species, thus resulting in the morphological similarity of them. However, the similarity of some morphological characters of C. davazamcii to those of C. korshinskii might result from the convergent adaptation to their common ecological environment.