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Changmaogu is a very rare and endangered rice landrace cultivated in a very limited area by Lama people, a branch of Bai ethnic group in Lanping County, Yunnan, China. No study on this precious landrace had been reported. This study was intended to explore the genetic diversity so as to develop strategy for conserving Changmaogu. The Changmaogu samples were compared with other three varieties (Hejing 16, Nipponbare and Hongxiangmi), using 24 pairs of SSR markers. Among all varieties, Changmaogu showed the richest genetic diversity. Cluster analysis also showed that Changmaogu can be distinguished in the genetic distance of 0.68. These data suggested that landrace is of great significance for the selection of rice varieties under the harsh environment and the acquisition of parents in the breeding work. The high altitude, low temperature and complex microbial community may be the important factors of genetic diversity in Changmaogu. The influence of 'agriculture-processing-marketing' mode of landraces should be continuously tracked. The strategy for conservation and sustainable development of Changmaogu was proposed in the present paper. [ABSTRACT FROM AUTHOR]