Abstract: Genetic diversity and population structure of ex-situ conservation populations from two remnant Isoetes sinensis populations and one remnant I.orientalis population were investigated using microsatellite markers.A total of 56 alleles were identified in 720 individuals across the seven microsatellites,with a mean value of 8.43 alleles per locus.High genetic diversity was found in subpopulations with the mean polymorphism information content(PIC) of 0.707.Low genetic differentiation was revealed among conservation subpopulations(G_ST = 0.070),which may be due to higher gene flow among ex-situ subpopulations(N_m=3.59).Gene flow between subpopulation pairs was significantly affected by the relative position and water flow state among subpopulations under ex-situ conservation.One-way ANOVA indicated that the dispersal ability of Iseotes spores or sporophytes along the main flow direction was stronger than that along the weak flow direction,which suggested water flow had a great impact on the gene flow of Isoetes.This was in accordance with UPGMA analysis,which revealed that the subpopulations tended to cluster with the neighbor subpopulations connected by water flow.The results indicated that genetic mixing or genetic assimilation may have occurred among ex-situ conservation populations from different remnant populations of I.sinensis and I.orientalis,suggesting a possible risk of out-breeding depression if genetic enhancement was implemented by translocation of individuals from different remnant populations.Therefore,translocation among these remnant populations with local adaptation or significant evolution is not recommended to construct ex-situ conservation or reintroduction populations.