Yushania niitakayamensis is distributed in Taiwan, south-west China and northern Philippines. In Taiwan, the species occurs in the central mountain ranges from 1500 to 3500 m in altitude. Morphological variation, especially in terms of plant height, is large, with plants ranging from 10 cm to 5 m in height. The species appears to spread mainly by rhizomes and flowers rarely, leading to the prediction that most populations are comprised of a single or a few clonal genotypes and that the observed morphological variation is primarily due to phenotypic plasticity. The purpose of the present study was to investigate the genetic structure of this species on Mt Hohuan in central Taiwan. Ten plants from a single clone and ten plants of unknown genetic background were surveyed at one site in order to select RAPD primers useful for clone identification. Plants at a second site were collected at 1-m intervals across a 50-m transect through the population. Plants at one extreme (exposed portion) of the transect were approximately 15–30 cm in height, whereas plants up to 410 cm in height were found at the other shaded end of the transect. Comparison of amplification profiles for 12 primers revealed that in contrast to our predictions of genetic uniformity, many samples had reproducibly different RAPD amplification profiles, with the 51 samples representing 31 clones. These data imply that the clone size is relatively small, and the population is actually highly diverse genetically. The genetic variation in this population may be due to a higher frequency of sexual reproduction during the evolutionary history of the species and/or a high somatic mutation rate for RAPD loci in clones of Yushania.