The Bird-Nest Fern Asplenium sect. Thamnopteris or A. nidus L. complex is defined by the synapomorphic character peculiar to Aspleniaceae, an anastomosing vein near the margin of the simple lamina. Thus, it is easily recognizable and its monophyly is quite clear. In spite of its naturalness as the whole group, species delimitation is very confusing. Three species of sect. Thamnopteris, A. antiquum Makino, A. australasicum (J. Smith) Hooker and A. nidus L. have been recognized in Japan, but the naturalness of each species is still not clear because their morphology is too simple to find good qualitative taxonomical characters. In the present work, we examined the intraspecific variation of allozymes and rbcL sequences in the Japanese plants of sect. Thamnopteris and compared them with those from other paleotropical localities in order to recognize natural units in such morphologically simple plants. We found a large amount of genetic variation in this section and inferred that A. antiquum is a species of ancient origin, though morphologically it is not so different from other species of the sect. Thamnopteris. It was also discovered that the so called A. australasicum in Japan has a very different rbcL sequence from A. australasicum sensu Holttum, which is distributed in Australia and South Pacific Islands. Based on these molecular data, we described the Japanese A. australasicum as a new species, Asplenium setoi N. Murak. et Seriz.