Great burdock (Arctium lappa L.) of the Compositae has economic importance in East Asian countries. In Taiwan, major cultivated areas are located in Gueilai Township, Pingtung County and Jiali Township, Tainan County. The present work was undertaken with two objectives of determining intraspecific genetic variations and studying the population dynamics of A. lappa L. In total, 23 individuals were collected from Gueilai (n = 15) and Jiali (n = 8). Chloroplast trnL-trnF intergenic spacer (IGS) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were subcloned and sequenced. Length variations among IGS sequences ranged from 805 to 808 bp and among ITS sequences ranged from 360 to 362 bp. Intraspecific genetic distances within IGS sequences ranged from 0 to 0.01 and within ITS sequences ranged from 0 to 0.023, which were lower than interspecific distances. All IGS and ITS sequences being separately scattered on each of the neighbor-joining trees with insignificant genetic differentiation indices (p > 0.05) suggested that both samples shared a recent common ancestor. Minimum spanning trees, Tajima’s and Fu’s parameters, and mismatch distributions implied that A. lappa L. had experienced a historical population expansion. Key words: Compositae, Gueilai, Jiali, genetic distance, population expansion.