Most wild rose species in the Netherlands belong to Rosa section Caninae (dogroses), with Rosa arvensis (section Synstylae) and Rosa spinosissima (section Pimpinellifoliae) as other indigenous species. All species are rare, often found in small populations or as scattered individuals, except for Rosa canina and Rosa corymbifera. Conservation strategies have been developed for these roses, with a focus on ex situ methods, including clonal archives and seed orchards, using vegetative propagation from the original shrubs. Efficient collection management aims at preservation of maximum genetic diversity with a minimum of duplicated genotypes. However, dogrose taxonomy is complex because of species hybridization, different ploidy levels, and their matroclinal inheritance due to Canina meiosis. They can also reproduce vegetatively through root suckers. In order to assess the genetic structure and the levels of genetic diversity and clonality within and among the wild rose populations in the Netherlands, we genotyped individuals in wild populations and accessions in the ex situ gene bank with 10 highly polymorphic microsatellite markers. The analysis revealed 337 distinct multilocus genotypes (MLGs) from 511 sampled individuals, with some MLGs shared across different species and sites. The genetic structure analysis showed distinct clusters separating non-dogrose species from the Caninae section. Geographic distribution of MLGs indicated both local and widespread occurrences. Redundancy analysis identified 152 distinct MLGs from 244 gene bank accessions, suggesting a 38% redundancy rate. Core collections were optimized to retain genetic diversity with minimal redundancy, selecting subsets of 20–40 individuals from different species groups. The study highlights the value of genetic characterization in guiding sampling strategies for dogroses. We propose a two-step approach that may be used to reveal clonality and redundancy and to optimize core collections of species that combine sexual and vegetative reproduction, to ...