Abstract: ISSR markers were used to measure genetic diversity of 72 individuals from four natural populations of Isoetes orientalis and I.sinensis,two rare and endangered fern species in China.A total of 98 DNA fragments were scored from the 11 ISSR primers and 66.33% percentages of polymorphic loci(PPL) was found.Lowlevel genetic diversity within both I.orientalis(8.16% and 7.14%) and I.sinensis populations(9.18% and 23.47%) was detected in the present study.AMOVA analysis indicated that for I.orientalis most of the variance(94.74%) resided within populations and for I.sinensis a greater amount of variation(86.71%) resided between populations.UPGMA cluster indicated that the individuals from two different species were distinct to each other.For I.orientalis the individuals for different populations did not cluster together.UPGMA cluster analysis also showed that there was distinct genetic differentiation between populations of I.sinensis.The probable causes that have contributed to the current pattern of genetic structure were discussed and the suggestions on the future protection of the Isoetes species were also given in the present study.