Topographic anaglyph images were viewed with red–cyan glasses, making it possible to recognize topographic relief features easily. Anaglyphs produced from digital elevation model (DEM) data are a very effective way of identifying tectonic geomorphology. This paper aims to re-examine tectonic geomorphology and to present new tectonic maps for the late Quaternary in and around the Kanto Plain and Nansei Islands. This is achieved by interpretation of an extensive area of topographic anaglyph images produced from 5-m- and 10-m-mesh inland DEMs of Japan provided by the Geospatial Information Authority of Japan, and 2-s- and 14-s-mesh DEMs of the seafloor. The 2-s-mesh DEM of the seafloor is processed from cloud point data of multi-beam echo-sounding devices provided by the Japan Agency for Marine-Earth Science and Technology and re-processed from digital bathymetric charts, with 1- to 2-m-interval counters of the Japan Hydrographic Association. The extensive area of topographic anaglyphs produced from combined detailed DEM are shown to be useful for identifying tectonic geomorphology in plain areas, as well as of the seafloor, when the “naked” topography is exaggerated vertically. We identified for the first time an active anticlinal broad deformation of the Yamanote tableland surfaces where the capital of Japan is located, as well as fault geomorphology associated with the left lateral strike–slip fault along the Ayasegawa fault in the Kanto Plain, which was believed to be a reverse fault. We also found that the marine terraces are tilted to the south at Okinoerabujima Island and eastward at Tokunoshima Island, in the middle of the Nansei Islands. These tilts are related to the reverse faults along the steep slopes of the islands’ shelves that are divided into the Okinawa trough to the west. These reverse faults, which were believed to be a normal fault from the geological research, are newly identified on the basis of the interpretation of the tectonic geomorphology on anaglyph images produced from detailed DEM of the seafloor.