One of the main research focuses of the Hortus botanicus Leiden is to study how the current biodiversity we see today, has originated, changed, and developed over time. The Hortus wants to study the relationship between species in specific focal taxa and see how they have diverged over time.

Within the plant kingdom occur many wondrous features such as carnivory or special floral traits related to specific pollinators and by comparing family members in an evolutionary framework, we aim to understand how these came to be. The systematic research at our garden uses a molecular phylogenetic approach to reconstruct the evolution of plants and other organisms. Several projects have focused on the evolution of specific plant groups (e.g., Annonaceae, Orchidaceae, Nepenthaceae, Phyllanthaceae). The reconstructed phylogenies are used to amend existing taxonomic classifications and to reconstruct the paths by which ecosystems have evolved by using trait evolution and historical biogeography.