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ABSTRACT: To study the genetic background of Evodia rutaecarpa by AFLP, and analyze the genetic diversity of E. rutaecarpa from different areas. E. rutaecarpa genomic DNA was extracted. The AFLP reaction system was established and AFLP primer pairs were chosen for the analysis. Forty-six individuals of E. rutaecarpa which from five provinces were analyzed by AFLP. The NTSYS-pc 2.1 software was used for cluster analysis. Six out of the original 72 pairs of primers were optimized for the study; AFLP analysis revealed the similarity coefficient of 0.53, the samples of E. rutaecarpa var. officinalis from Zhejiang province was separated from other accessions; E. rutaecarpa var. officinalis also showed more pronounced genetic variation than the E. rutaecarpa, and strong geo-related relevance. Variance of genetic background of E. rutaecarpa are large, AFLP analysis method can obviously identify different varieties of E. rutaecarpa, and can detect the genetic characteristics of inter-regional differences.Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica 02/2012; 37(3):278-82.