The genetic diversity of endangered plants is still largely unknown and rarely influences conservation plans. A perfect example of this situation is found in Geneva. Out of 270 threatened taxa, only two have been genetically studied. To provide new information on this essential genetic diversity, we used HTS approaches and the Hyb-Seq technique with the universal sequence capture probe set Angiosperms353. Being originally designed for phylogenetic studies, the potential of this probe set for conservation genomics, particularly for small, threatened populations, has been so far little explored. In this context, we analysed the population genetic diversity of three endangered species in Geneva: Balckstonia acuminata, Eryngium campestre and Lythrum hyssopifolia. On average, more than 900 unlinked SNPs were recovered. This number made it possible to analyse the genetic diversity, structure, and historical demography of the populations. Fst, although low, revealed significant differentiation between subpopulations. Notable heterozygosity for B. acuminata(0.95) and L. hyssopifolia (050) highlighted the possibility of hybridisation and polyploidy, respectively. In addition, Tajima's D detected bottleneck events for B. acuminata and E. campestre. PCA revealed significant distinctions between the two studied subpopulations of B. acuminata. Additionally, for E. campestre, the subpopulation located on the left side of the Rhône River exhibited a distinct clustering pattern compared to the subpopulations on the right side of the Rhône. By contrast, only E. campestre showed clustering in the STRUCTURE analyses. Discussions on the most appropriate conservation strategies for these species are guided by these new insights.