Populations of plant species at their geographic range limits often suffer from low levels of genetic diversity caused by fragmentation, genetic drift, restricted gene flow, inbreeding or vegetative reproduction. We assessed the reproduction mode, allozyme diversity, differentiation and spatial genotypic structure in four Estonian remnant subpopulations and three small and isolated Latvian populations of Astragalus arenarius (Fabaceae) at the northern edge of the species' range. Plants of all populations had a clear clonal structure with same multilocus genotypes (MLGs) growing sequentially and alternately with different MLGs. The number of MLGs among populations varied between 1 and 13, with the longest genets extending over 30 m. The populations were highly differentiated with no common MLGs shared. Sexual reproduction in the studied populations was severely reduced. The generative reproduction was modest and variable in different years. Our results show that the small fragmented populations of A. arenarius have a low genotypic richness. Extensive clonal propagation of the few surviving genets has evidently contributed to their persistence. Conservation measures for the endangered populations are discussed.