The genus Oxygyne comprises three species disjunctly distributed in Africa and Japan and is the least examined genus of the Burmanniaceae due to the scarcity of living material. We obtained living samples of Oxygyne shinzatoi and examined the phylogenetic position of this species on the basis on the 18S rDNA sequence. Oxygne shinzatoi was consistently found to belong to the monophyletic group of tribe Thismieae, but its position in the tribe differed depending on the criteria applied (maximum parsimony, maximum likelihood, Bayesian inference). Distance analysis from the most recent common ancestor indicated that O. shinzatoi had the lowest substitution rate among the species of tribe Thismieae. Combined with recent knowledge of basic chromosome numbers and substitution rate characteristics, O. shinzatoi can be considered to be one of the basal taxon of tribe Thismieae.