Abstract: In order to reveal the distribution pattern of genetic variation and haplotype geographical distribution pattern of Allium macrostemon,and to infer the refugia in the quaternary glaciation,the chloroplast gene fragments（psb A-trn H,rps16 and trn L-F）and nuclear gene fragments（ITS）of A.macrostemon in 14 regions of China were analyzed respectively.The results showed that the genetic diversity of A.macrostemon chloroplast gene（cp DNA）was lower than that of nuclear gene（nr DNA）（cp DNA:H_T=0.868;nr DNA:H_T=0.890）.The AMOVA analysis of cp DNA and nr DNA showed that the genetic variations occurred mainly among populations（cp DNA:92.84%;nr DNA:98.40%）,there was significant genetic differentiation among populations(cp DNA:N_st=0.918,G_st=0.866,F_st=0.928;nr DNA:N_st=0.984,G_st=0.855,F_st=0.984),and had an obviousphylogeographical structure in A.macrostemon populations（N＞G）.A total of 11 chloroplast and 14 nuclear haplotypes were identified in the A.macrostemon populations.The haplotype network and geographical distribution map showed that the chloroplast haplotype H3 and nuclear DNA genotype H1 had the highest frequency and were located in the center of the network structure,which might be the ancient haplotype.In addition,the glacial refuge hypothesis suggested that the region with high genetic diversity,ancient haplotype and more endemic haplotype might be the glacial refugia of A.macrostemon.Therefore,it was speculated that in the quaternary glaciation,A.macrostemon might be multiple glacial refuges in Dapanshan,Tianshui and Tonghua.The analysis could provide references for the evolution of similar herbs and enrich our understanding of the molecular phylogeography of herbaceous plants in East Asia.