Isolepis crassiuscula Hook. f. is distributed in Japan, Indonesia, Papua New Guinea, Australia and New Zealand. In Japan, I. crassiuscula is found only in Shirakawa-shi, Fukushima Prefecture, and is listed in Endangered Species List of Japan. The origin and phylogenetic relationships of Japanese I. crassiuscula was investigated using chloroplast DNA sequence data. The chromosome number of I/, crassiuscula was 2n = 96, which was the highest number in the genus Isolepis. Relationships among ten species of Isolepis are explored using rbcL and trnL intron sequence data. Our molecular data show a close phylogenetic relationship between Japanese and Australian I. crassiuscula.