The Pleistocene floristic change in the Northern Hemisphere is marked by extensive extinctions of Tertiary relicts in middle to high latitudes, which are thought to have been moderate in East Asia. However, species losses from geographically isolated areas in East Asia were comparatively heavy. In this study, we report a selective extinction event within the relict genus Staphylea (Staphyleaceae) from the Japanese Pleistocene. We described two species, Staphylea bumalda DC. and S. spinosa Y. Huang et A. Momohara sp. nov. (Staphyleaceae), based on seed remains from the middle early Pleistocene (ca. 1.7-12 Ma) Shobudani Formation in the northern Kii Peninsula of southwestern Honshu. According to the fossil records and modern distributions of Staphylea, we presumed that S. bumalda emerged in Japan at least by the early Pliocene and has persisted until today, whereas S. spinosa was exterminated after the middle early Pleistocene. To explain the different fates of the two species, we estimated their climate tolerance by observing the climate requirements of their nearest living relatives. Our results indicate that S. bumalda could tolerate colder climates, particularly in winter, than S. spinosa. Floristic compositional changes at the study area reveal a cooling trend followed by a glacial stage after the last occurrence of S. spinosa. The cold winter temperature in the glacial stage was probably beyond the cold tolerance of S. spinosa, which ultimately led to its demise. Surrounding geomorphological changes, such as the uplift of the Kii Mountains, might also have played a role in the way of preventing plant migration when climate deteriorated. This selective extinction event adds a new episode into our knowledge of the Pleistocene plant extinctions along with their possible underlying mechanisms in the Northern Hemisphere. (C) 2018 Elsevier B.V. All rights reserved.