A nearly complete mandible of a large ochotonid lagomorph was recently found from upper Lower Miocene deposits in central Japan, and it is described as a new species, Alloptox japonicus. The new species can be distinguished easily from all known species of the genus by size and several distinct characters of the p3 occlusal pattern. Almost all of these features show opposite character states in other species of Alloptox, suggesting distinction at the subgeneric level, and a new subgenus, Mizuhoptox, is created for A. japonicus. All previously known species are included in the subgenus Alloptox. Geologic age of the new species is about 17.6 (between 18 and 17.5) Ma (late Early Miocene), which is almost the same as A. sihongensis, the smallest and probably earliest species in continental Asia, suggesting that the distinction between those two subgenera was present at an early stage of Alloptox evolution.