Abstract:To explore the relationship and biogeographic distribution pattern of A. macrostemon in different areas of Southwest China, we compared and analyzed 27 nrDNA ITS sequences of A. macrostemon, of which 21 were newly generated and 6 from GenBank. The results showed: (1) the sequence length of the A. macrostemon Bunge varied from 607-638 bp and the GC content of 48%-52%, with an average 50%. (2) A. macrostemon is monophyletic basing on Bayesian inference and Maximumparsimony analysis. (3) Phylogenetic analysis indicated that the 27 populations are generally divided into group a and group b. Among them, Jiange County, Sichuan, Wixi County, Chongqing, Dejiang County, Guizhou and Qiubei County, Yunnan, located in the east of Southwest China, are clustered into group a; Wenchuan, Shimian, Jiangyou of Sichuan Province and Hutiaoxia, Kunming, Sanba of Yunnan Province located in the west of Southwest China belongs to group b. The results suggested that nrDNA ITS sequence could identify the relationship of A. macrostemon in different regions.