Abstract: By using inter-simple sequence repeat (ISSR) makers, this paper studied the genetic diversity and clonal structure of two Potamogeton malaianus populations growing in different habitats of two lakes in the middle reaches of Yangtze River.With six primers selected, a total of 40 fragments, of which 30 (75.0%) were polymorphic, were obtained from 106 individuals. This species showed a high genetic diversity, with Nei’s gene diversity of H=0.2471 and Shannon’s information index of I=0.3736. A low degree of population differentiation (G_st=0.0861) was found between the two populations, and a very high clonal diversity (D=0.9917) was detected, according to the analysis based on the polymorphic loci. No common genotypes were found among the individuals from the two populations, showing a great clonal differentiation between them. The spatial distribution pattern of P. malaianus genets showed ‘guerilla’ architecture, and the clonal distance of the population in lake center (3.0～31.5 m) was significantly larger than that in lakeshore (2.4～6.7 m).

Key words: Biogeochemistry, Grassland ecosystem, Storage, Biogeochemical cycle