Biodiversity is declining at alarming rates and requires urgent conservation measures for maintaining ecosystem functionality. Despite its importance, the phylogenetic aspect of biodiversity is often neglected. The objective of this doctoral thesis was to provide a phylogenomic framework for the regional flora of the Geneva canton in Switzerland, and use it to complement ongoing biodiversity assessments. Here, we proposed a complete methodology and used it to generate a highly resolved phylogenetic tree comprising most of the 1,098 flowering plant species composing the regional flora. This phylogenetic framework was then used to estimate the loss of evolutionary history caused by the human-mediated transformation of the landscape. Further, the phylogeny-based approach has allowed the identification of priority species, areas, and habitats to mitigate future losses of evolutionary history. Finally, we found that urbanization decreases phylogenetic richness but increases phylogenetic turnover across plant communities in the Geneva agglomeration.