Luronium natans (L.) Raf. or Floating Water-plantain, an aquatic perennial, is endemic to west and central Europe. In Belgium, the number of sites with L. natans decreased markedly in the 20th century. The species is considered “vulnerable” on the national Red List and its conservation status as “unfavourable”. Considering its mixed reproduction strategy and polyploidy, population genetics could provide insight into its genetic vulnerability. We investigated genetic variation within and among 30 locations from various habitats in Flanders using amplified fragment length polymorphic markers. Besides information on clonality and genetic diversity, we tried to include information on (former) population connectivity. We found a high degree of clonal reproduction in the investigated locations. Mostly, a dominant multilocus lineage (clone) was shared among patches within a water body. But also an occasional clone was found among distant locations. Nevertheless, populations of L. natans were highly differentiated, but proved to be generally low in genetic diversity. It appears several populations were founded by one or a few migrants from neighbouring populations and were able to persist mainly through asexual reproduction. Although census population size and genetic diversity are related, clonal reproduction confounds this trend. Considering the strong population dynamics, periodical evaluation of the within-population genetic diversity is necessary to gain insight in the importance of sexual reproduction and seed bank recruitment.