Abstract Three chloroplast DNA regions ( mat K, rbc L and trn H- psb A) were used to analyze the phylogenetic relationships and maternal donor of Kengyilia species and their closely related species. The Maximum Parsimony, Bayesian Inference and TCS network phylogenetic reconstructions partitioned the species into three reciprocally monophyletic groups. Kengyilia kokonorica , Kengyilia melanthera , K. melanthera var. tahopaica , Kengyilia mutica , and Kengyilia thoroldiana were related to species of Agropyron , whereas Kengyilia alatavica, Kengyilia batalinii , Kengyilia gobicola , Kengyilia kaschgarica , Kengyilia longiglumis , Kengyilia nana , Kengyilia stenachyra , Kengyilia tahelacana , and Kengyilia zhaosuensis were related to species of Pseudoroegneria and Roegneria. In addition, Kengyilia grandiglumis , Kengyilia hirsuta , Kengyilia laxiflora , and Kengyilia rigidula were related to species of Pseudoroegneria and Roegneria in phylogenetic analyses of mat K and rbc L, but to species of Agropyron in phylogenetic analyses of trn H- psb A. These results indicate that there have been at least two phylogenetically divergent maternal donors within Kengyilia , i.e. Agropyron (P genome) and Roegneria (StY genome).