Isoetes L., the single remaining genus of the family Isoetaceae, is a cosmopolitan genus of heterosporous lycopods comprising 200 or more species. Isoetes hypsophila Hand.-Mazz., an

alpine quillwort endemic to the southeastern Qinghai-Tibetan (Q-T) Plateau, is a diploid species (2 n = 22) distributed in shallow zones of plateau lakes or marshes of Sichuan and Yunnan provinces in China ( Chen et al., 2005 ). Field surveys over the past eight years identifi ed six geographically isolated regions with small populations, which are Hongyuan, Baiyu, Jiulong, Litang, and Daocheng counties in Sichuan Province and Shangri-La County in Yunnan Province ( Chen et al., 2005 ; Chen et al., 2010 ). Like other quillwort species in China, such as I. yunguiensis Q. F. Wang & W. C. Taylor, I. taiwanensis De Vol , I. orientalis Hong Liu & Q. F. Wang, and I. sinensis Palmer, I. hypsophila is endangered because of habitat degradation and loss, water pollution and eutrophication, competitive exclusion, and human disturbance ( Liu et al., 2005 ), and the genus Isoetes is listed in the fi rst category of the key protected wild plants in China ( Yu, 1999 ). Considering that I. hypsophila played an important role in the evolutionary history of quillworts and occupies a basal position among East Asian and eastern Australian members of the genus ( Taylor et al., 2004 ), an appropriate conservation program is urgently needed to prevent further loss of I. hypsophila . Therefore, it is essential to develop molecular markers for the population genetic analysis of I. hypsophila and other Chinese quillworts to provide essential information for the development of a management and conservation strategy. Among various molecular marker tools, microsatellite markers have proven to be highly effi cient molecular tools for population genetic studies, due to their high reproducibility, multiallelic nature, codominant inheritance, relative abundance, and wide genome coverage. In this study, nine highly variable microsatellite loci were developed for the endangered I. hypsophila , and their cross-amplifi cation in I. sinensis was examined.