Abstract: Random Amplified Polymorphic DNA (RAPD) markers were used to measure genetic diversity of 48 individuals from four natural populations of Isoetes sinensis，　a rare and endangered plant in China. A total of 124 DNA fragments were scored from 14 RAPD primers, of which 58.06% were polymorphic. A low level of genetic diversity within populations was detected, with PPB (percentage of polymorphic bands) values ranging from 0.81% to 12.90%. An Analysis of Molecular Variance (AMOVA) was used to apportion the variation within and among populations. Results indicated that most of the variation (58.9%) resided among populations and a small amount of variation (41.1%) represented differences within populations. Inbreeding is likely the factor that results in the low level of genetic diversity within the populations. Genetic drift and limited gene flow might also have enhanced genetic differentiation among the populations. In view of the ecological and genetic information available for I. sinensis,we suggest establishing as many in situ conservation spots as possible and cross transplanting plants or seedlings mutually among populations in order to enhance gene flow. By this means, the genetic diversity resources of I. sinensis can be preserved to the greatest extent.