Ottelia acuminata (Gagnep.) Dandy, an economically and ecologically important aquatic herb, is mainly distributed in southwestern China, having been recorded in Yunnan, Hainan, Sichuan, Guizhou, and Guangxi provinces ( Li, 1981 ). It has been used as an ornamental and an edible plant in Yunnan Province. In recent years, due to water pollution in their habitats, excessive collecting, and the ravages of the imported grass carp, populations of O . acuminata have declined rapidly and have even disappeared from many locations in China. Ottelia acuminata has been recognized as an endangered species in China ( SEPA and IBCAS, 1987 ). An understanding of the levels and distribution of genetic variation in endangered species can inform us of their evolutionary history, and can also help us develop appropriate conservation and management strategies for these species ( Frankham et al., 2002 ). Until now, there have been only a few population genetics studies on the endangered species O . acuminata , and these studies have all been based on dominant molecular markers, e.g., inter-simple sequence repeat (ISSR) markers ( Zhang et al., 2009 ; Long et al., 2010 ). Here, we report the development and characterization of eight polymorphic microsatellite loci from O . acuminata , which will facilitate ongoing studies of genetic diversity and sustainable conservation for this endangered species.