The phylogenetic relationship of Atractylodes lancea, A. chinensis, A. koreana, A. ovata and A. japonica were analyzed by comparing the 2.6 kb sequence in a chloroplast gene trnK encoding tRNA^Lys (UUU). The dried rhizomes of the former three species have been used as the crude drug "So-jutsu" and those of the latter two as "Byaku-jutsu" in Chinese and Japanese traditional medicine ("Kampo-medicine"). The trnK phylogenetic tree revealed that A. ovata is an outgroup of the five Atractylodes species examined and that A. japonica and A. lancea are most closely related. PCR amplification of trnK with HinfI digestion provided us with a simple method to distinguish A. ovata from other Atractylodes species at the molecular level.