Herpetofauna, particularly amphibians and reptiles, exhibit high levels of endemism and distinct diversity pattern on Taiwan island. However, the biogeographic history of these groups remains obscure, in part due to the lack of a herpetofaunal fossil record. Here, we report the first fossil record of frogs and snakes from Taiwan, based on Middle Pleistocene vertebrate assemblage recovered from the Chochen–Tsailiao area in southern Taiwan. The collection includes a vertebra of a bufonid frog and multiple vertebrae of colubrid and viperid snakes. Despite their fragmentary preservation, several vertebrae are identifiable, including a toad (Duttaphrynus melanostictus), rat snakes (Elaphe sp., Ptyas mucosa, and P. cf. mucosa), a wolf snake (Lycodon rufozonatum), and a pit viper (Protobothrops sp.). Additional vertebrae are attributed to Alethinophidia indet. The preservation of these delicate skeletal elements in a tectonically active and humid subtropical setting highlights the exceptional nature of this discovery. Palaeoenvironmental reconstruction based on ecological preferences of extant analogues suggests that the region supported a humid fluvial and open woodland environment with abundant water bodies.