Morphological and cuticular features of Cunninghamia protokonishii were examined by studying the original material and additional fossils that were collected from the lowest Miocene to the lower Pleistocene of Japan and Korea. The species is characterized by foliar morphology that superficially resembles C. konishii, but differs by large terminal seed cones and seeds, which are more similar to C. lanceolata. Cuticle of C. protokonishii shows a wide range of anatomical variability compared to the two extant species that includes epidermal cell size, stomata distribution, and orientation. Based on foliar morphology, C. protokonishii can be distinguished from all other known fossil and extant species of Cunninghamia described so far. Distribution of C. protokonishii was mostly confined to the Japanese islands, with neighboring areas in Korea and southern Sakhalin. It appeared in eastern Asia by the earliest Miocene—a time prior to the opening of the Sea of Japan—and persisted until the Mio-Pliocene on the Japanese islands.