Seagrasses are marine angiosperms that form seagrass beds in shallow coastal areas and are known to provide a wide range of direct and indirect ecosystem services to humans. Surfgrasses (Phyllospadix spp., Zosteraceae) occur in rocky intertidal to subtidal zones of the temperate and subarctic North Pacific among which Phyllospadix iwatensis Makino and P. japonicus Makino occur in Japan. Due to their limited and endemic distribution in Japan and the surrounding region, and their declining range and population, these two species are listed as threatened in the IUCN Red List of Threatened Species (VU for P. iwatensis and EN for P. japonicus). On the Pacific coast of Japan, the northern species P. iwatensis occurs from Chiba to Hokkaido and the southern species P. japonicus occurs from Mie to Ibaraki, and thus the distributions of these two species overlap in Chiba and Ibaraki, whereas their distribution on the Japan Sea coast is relatively understudied and remains unclear. These two species may divide their distributions due to differences in habitat preference, especially in seawater temperature. As ongoing climate change continues, it is expected that surfgrass distributions will change with temperature rise. To consider their conservation, it would be important to understand how surfgrass distributions are determined and to predict how they change in the future. In this study, we use a species distribution model to estimate the current distribution of two surfgrass species in Japan using species occurrence data from museum specimens and observation records, including the authors’ personal observation data, and environmental variables such as seawater temperature, bottom slope, wave exposure, and geological substrates. Using the species distribution model for current surfgrass distribution, we further apply the model to predict future changes in their distribution under different Representative Concentration Pathways (RCP) scenarios. Based on the results obtained, we will discuss potential impacts of distribution changes and adaptation methods for their conservation.