The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. However, there is no consensus on the origin of the choana despite decades of heated debate; some have claimed that it represents a palatally displaced external nostril, but others have argued that this is implausible because it implies breaking and rejoining the maxillary-premaxillary dental arcade and the maxillary branch of nerve V. The fossil record has not resolved the dispute, because the choana is fully developed in known tetrapod stem-group members. Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.