Abstract: The phylogenesis of Iris L. was analyzed using the chloroplast genes rbcL. Classification was performed with maximum parsimony method and the gene tree were constructed with Crocosmia crocosmiflora as outgroup, 21 wild populations of Iris L. from China and download 49 sequences from GenBank. As for disputed species, clustering trees results showed Iris lactea var. chinensis(Fisch.) Koidz. had close relationship with Iris lactea Pall.. Iris confusa Sealy had more close relationship with Iris japonica Thunb. than that with Iris wattii Baker. Iris goniocarpa var. tenella Y.T. Zhao was very relevant to Iris goniocarpa Baker, but Iris goniocarpa var. grossa Y.T. Zhao was distant. Iris sichuanensis Y.T. Zhao and Iris leptophylla Lingelsh. were closely related. Clustering relationships of Series Sibirica were very complexed, and genetic relationgships were not clear.