Abstract: By using inter-simple sequence(ISSR) markers,this paper studied the genetic diversity and clonal structure of two Heleocharis valleculosa f.setosa populations(120 individuals) in Poyang Lake.By five primers,85 fragments were amplified,of which 49(57.65%) were polymorphic.As a result,a relatively high level of genetic diversity was revealed(H=0.1545,I=0.2400,at species level),but a low level of genetic differentiation was detected between the two populations(G_ST=0.0201).High clonal diversity was detected but no common genotype found between the two populations,which meant great clonal differentiation.In both populations,the spatial genetic structure were found as a random mode.