The Botanical Garden comprises the main garden, Koishikawa Botanical Garden, in Hakusan, Bunkyo-ku, Tokyo, and the Nikko Botanical Garden branch in Nikko, Tochigi Prefecture. Together, the two gardens maintain around 6,000 species of wild plants and have a collection of about 800,000 herbarium specimens, including 5,000 types. Koishikawa Botanical Garden has a large glasshouse and a cold temperate room where tropical and cool-temperate plants from various regions of the world are cultivated for research purposes. The Koishikawa garden conducts ecological and taxonomic research focusing on the evolution of angiosperm pollination systems. Notable studies include the discovery of pollination mutualism between Phyllanthaceae plants and Epicephala moths, the identification of plants pollinated by fungus gnats and the determination of the defensive role of lobed leaves against herbivores. With the support of modern approaches such as next-generation sequencing, the historical herbarium collection at the Koishikawa Botanical Garden serves as a valuable resource for phylo-taxonomic studies, fostering global collaboration and enabling the discovery of plant lineages new to science. The Nikko garden aims to elucidate the diverse adaptation strategies of plants to their native environments by measuring physiological and ecological properties, such as photosynthetic capacity and water use. For instance, we are now investigating the physiological responses of evergreen conifers to low temperatures and frost drought as well as the functions of various morphological and anatomical traits. These factors lead to interspecific variation in the adaptation strategy and geographic distribution along elevation gradients. Research on plant diversity uses a variety of approaches, including fieldwork in native habitats, morphological and chemical analyses, and molecular phylogenetic analyses. This makes use of the extensive plant collections and research facilities in the Koishikawa and Nikko gardens.