Abstract: This study surveys genetic variations in two emergent species that differ in pollination mechanism, breeding system, and extent of sexual reproductive success.The assay of vertical slab polyacrylamide gel electrophoresis was used to quantify allozyme variability in 3 populations of the entomophilous outcrossing Butomus umbellatus L.and 4 populations of the pseudo-cleistogamy inbreeding Limnocharis flava (Linn.) Buch.based on 19 and 21 readable loci of 9 enzyme systems, respectively.Electrophoretic data showed that the populations of both species have relatively high levels of genetic diversity, low levels of genetic differentiation than other investigated aquatic taxa, quite the contrary compared with the same breeding system terrestrial taxa, probably due to isolated habitat.Population genetic diversity of B.umbellatus (A=1.35, P= 0.381, and H_e=0.144) was greater than of L.flava (A=1.30, P=0.320, and H_e=0.076), and population differentiation of B.umbellatus (G_st=0.200) was lower than of L.flava (G_st=0.391).The results were attributed to the difference in breeding systems.These data indicated that the breeding system of B.umbellatus is outcros sing (Outcrossing rate t=94.0%), yet the breeding system of L.flava is mixed selfing and outcrossing (t=58.5%) in which there seem to be a shift.The gene flow (N_m) in the two species was 0.998 and 0.390, respectively.