Nymphoides peltata is a distylous aquatic plant. In order to explore the relative importance of clonal growth and sexual reproduction within populations and also to reveal the origin of the commonly occurring one style morph populations in China, we studied the clonal diversity and population genetic structure of this species. By using seven single sequence repeat primer pairs, a total of 192 multilocus genotypes (MLGs) were identified among the 472 samples from the 21 populations analyzed; each population had two or more MLGs. The number of MLGs was lower for the one style morph populations than distylous populations. Analysis of molecular variance showed that a smaller proportion of genetic variation resided among populations (36.8%). A neighbor-joining tree indicated that there was no significant geographical structure of the genetic variation among populations of N. peltata. The Bottleneck tests indicated that there had been significant bottlenecks in most of the studied populations. The successful sexual recruitment from seeds may have contributed to the high clonal diversity in distylous populations of N. peltata in China. Demographic stochasticity or bottleneck should account for the one style morph population with several MLGs. And also the bottleneck effects or demographic changes caused by human activities occurring randomly in populations should account for the finding of no significant geographical structure of the genetic variation among the investigated populations of N. peltata.