Rosa spinosissima L. is part of the highly dynamic coastal habitat of the Wadden Sea, between the coast of northwestern continental Europe and the Frisian Islands. Plants of this species grow clonally via root suckers to form large patches, which stabilize dunes and help to protect the islands and used for this purpose locally on the island Sylt. Rosa spinosissima plants are affected by both water and wind in their harsh environment, and are threatened by human impact via habitat destruction and introduction of foreign species. In these northern parts of its range R. spinosissima is categorized as endangered. The population structure of R. spinosissima was investigated using ten microsatellite loci and 195 individuals of Frisian Island populations and European coastal continental samples. DAPC, Kmeans and Structure analyses were conducted to study the genetic composition and integrity of these natural populations relative to cultivated and nursery material mostly consisting of central continental genotypes. The DAPC and Structure analyses differentiated populations of the Frisian Islands between each other and separated them from nursery samples, but some natural populations showing an impact of nursery and cultivated genotypes. In addition, some clonal patches of R. spinosissima were detected. Our results show that the natural Frisian Island populations of R. spinosissima are threatened by the introduction of nonadaptive genotypes into the gene pool.