Across Japan, populations of Sika deer (Cervus nippon) have grown rapidly over recent decades, and Odaigahara has particularly high densities of Sika deer. In Odaigahara, this overpopulation has led to changes in stream flow and riparian landscapes, with formerly diverse communities of dwarf bamboo growing increasingly homogenous. Lower-layer vegetation (Sasamorpha borealis, Sasa nipponica, bryophytes) that had covered Odaigahara disappeared, the number of trees of higher-layer vegetation decreased, and the landscape changed from a humid, dense landscape to a bright, homogenous landscape. Vegetation plays an important role in the succession of benthic invertebrates in streams. In this study, we examined changes in the benthic invertebrate assemblages of Odaigahara and related them to vegetation history. In 2006, there were fewer individuals and genera of benthic invertebrates than in 1983. Benthic invertebrate composition also differed from 1983 and the degree of difference varied by stream basin. The abundance of Ephemeroptera (e.g. Drunella spp.) was decreased and of Plecoptera (e.g. Sweltsa spp.) was increased. Over the same period, lower-layer vegetation and humidity decreased while temperature increased; these factors also likely contribute to the observed changes to benthic invertebrate assemblages.Implications for conservation: The forests of Odaigahara are still subject to complex factors such as sika deer, human activities and global environmental changes. Comparison of current and historical benthic invertebrate communities will help to identify the restoration goals for the forest ecosystems necessary for benthic invertebrate communities. Proper management of deer and conservation of remnant vegetation, including rhizomes, in the Odaigahara will contribute to the maintenance of the present and future benthic invertebrate community.