The University of Tokyo Chiba Forest was established in the southern Boso Peninsula in 1894 as the first university forest in Japan. The forest has an area of 2,169 ha and is located in a warm-temperate forest zone. The area is covered with various tree types. Planted forest consists of Cryptomeria japonica and Chamaecyparis obtusa. Coniferous natural forest is mainly dominated by Abies firma and evergreen Quercus spp.

The University of Tokyo Hokkaido Forest, which has an area of 22,708 ha and is located in central Hokkaido, is dominated by boreal coniferous trees mixed with broad-leaved deciduous trees.

The University of Tokyo Chichibu Forest has an area of 5,812 ha and is located in Chichibu-Tama-Kai National Park. It is in a cool-temperate zone with mountainous terrain. The vast majority of the UTCF (>85% of the total area) is covered with natural forest. The major tree species are Abies firma, Tsuga sieboldii, Fagus japonica, and Fagus crenata. Of the 28 Acer species in Japan, 20 are found in the UTCF.

The University of Tokyo Tanashi Forest is the nearest university forest to the University of Tokyo campus and is approximately 8 ha in area.

Ecohydrology is an interdisciplinary field studying the interactions between forest and water, and their ecosystem services. The ERI manages the Akazu Research Forest (ARF, 745 ha), the Inuyama Research Forest (IRF, 442 ha), and the Ananomiya Experimental Forest (AEF, 77 ha) for various field researches and educations.

Fuji Iyashinomori Woodland Study Center is 40 ha in area and located on the eastern slope of Mt. Fuji. The area lies on the higher cool-temperate forest zones.

The Arboricultural Research Institute is 247 ha in area and located at the southern tip of the Izu Peninsula. It is in a typical warm-temperate forest covered with evergreen tree species. Field adaptation tests have been conducted over several decades to select locally adaptable Eucalyptus species. Further screening of candidate species is planned to identify better species in terms of tree growth.