Toyotamaphimeia is an extinct crocodylian lineage whose name is derived from a mythological Japanese princess. Here, we re-examine the type specimens of a long-forgotten species: Tomistoma taiwanicus from the Pleistocene of Tainan (Taiwan) and revise its taxonomic status to Toyotamaphimeia taiwanicus n. comb., leading to the first recognized species of Toyotamaphimeia outside Japan. Our phylogenetic analyses also support this taxonomic assignment and, more interestingly, further suggest an East Asian lineage. In addition, Toyotamaphimeia taiwanicus n. comb. represents a tropical species, resolving a long-standing puzzle of why Toyotamaphimeia only inhabited a much higher latitudinal area (Japan). Given the large body size of Toyotamaphimeia taiwanicus n. comb. (∼7 m) and the fact that it is geologically older than Toyotamaphimeia machikanensis from Japan, we propose a novel evolutionary scenario: the genus Toyotamaphimeia originated in Taiwan and evolved to a large body size with gigantothermic physiology, which resulted in migration out of Taiwan and dispersal farther north to Japan. Our taxonomic identification shows the presence of an extinct endemic crocodylian species from the Pleistocene of Taiwan with large-scale paleogeographic implications. This study, with our recent progress in vertebrate paleontology in Taiwan, should provoke more in-depth paleontological research on the Pleistocene extinction.