The Philippine crocodile was described in 1935 by Karl Schmidt on the basis of a type specimen and three paratypes from the island of Mindoro (Schmidt 1935, 1938). Schmidt also described the closely related New Guinea freshwater crocodile (Crocodylus novaeguineae) in 1928 and later made a comparison of morphological differences between C. mindorensis, C. novaeguineae and C. porosus, maintaining C. mindorensis as a separate species (1956). However the Philippine crocodile has long been treated as C. novaeguineae mindorensis, a sub-species of the New Guinea crocodile, by other authorities. Hall (1989) provided new evidence of the distinctness of the Philippine crocodile and nowadays C. mindorensis is generally treated as a full species endemic to the Philippines.