Lycoris longituba Y. Hsu et Q. J. Fan is a perennial, bulbiferous, herbaceous plant of the family Amaryllidaceae. It is endemic in China, with a very limited distribution, being found only at Langyashan in Anhui province, and Baohuashan and Xuyi city in Jiangsu province, all located about 50 km from one another (see figure 1 and table 1 in electronic supplementary material at http://www.ias.ac.in/jgenet/). A unique biological characteristic of this plant is that its leaves come out in spring and die in early summer, followed by flowering. Thus, its vegetative growth and reproduction are discrete, which is rare in angiosperms. With a vigorous and long scape, its flowers are diverse in both colour and floral form, and fragrant in smell, and have high ornamental value. Also called Chinese tulip, this species is ideal for ikebana, and its bulb has medicinal properties. We have collected more than 70 variants of this species in our laboratory with different floral colours and forms. Population-genetic structure is considered as spatiotemporal distribution of genetic variation (Ge 1997), and reflects evolutionary processes in populations (Hamrick and Loveless 1989). To take right measures to protect wild resources of L. longituba, it is important to study the range of genetic variation, genetic structure, diversification trend and other factors affecting genetic structure of the populations of this important and sparsely distributed species. Presently, many biochemical and DNA-based markers are used in studies of population structure. The random amplified polymorphic DNA (RAPD) method (Williams et al. 1990) is frequently applied to reveal population-genetic variation, divergence and biogeography (Schaal and Leverich 2001). A large number of studies have successfully applied this method to study genetic variation in plants owing to