Members of the Eya family, which are a class of transcription factors with phosphatase activity, are widely expressed in cranial sensory organs during development. However, it is unclear whether these genes are expressed in the taste system during development and whether they play any role in specifying taste cell fate. In this study, we report thatEya1is not expressed during embryonic tongue development but thatEya1-expressing progenitors in somites or pharyngeal endoderm give rise to tongue musculature or taste organs, respectively. In theEya1-deficient tongues, these progenitors do not proliferate properly, resulting in a smaller tongue at birth, impaired growth of taste papillae, and disrupted expression ofSix1in the papillary epithelium. On the other hand,Eya2is specifically expressed in endoderm-derived circumvallate and foliate papillae located on the posterior tongue during development. In adult tongues,Eya1is predominantly expressed in IP3R3-positive taste cells in the taste buds of the circumvallate and foliate papillae, whileEya2is persistently expressed in these papillae at higher levels in some epithelial progenitors and at lower levels in some taste cells. We found that conditional knockout ofEya1in the third week orEya2 knockout reduced Pou2f3+, Six1+and IP3R3+taste cells. Our data define for the first time the expression patterns ofEya1andEya2during the development and maintenance of the mouse taste system and suggest thatEya1andEya2may act together to promote lineage commitment of taste cell subtypes.