BackgroundPrevious studies have claimed that pharyngeal teeth in medaka (Oryzias latipes) are induced independent of retinoic acid (RA) signaling, unlike in zebrafish (Danio rerio). In zebrafish, pharyngeal tooth formation depends on a proper physical contact between the embryonic endodermal pouch anterior to the site of tooth formation, and the adjacent ectodermal cleft, an RA‐dependent process. Here, we test the hypothesis that a proper pouch–cleft contact is required for pharyngeal tooth formation in embryonic medaka, as it is in zebrafish. We used 4‐[diethylamino]benzaldehyde (DEAB) to pharmacologically inhibit RA production, and thus pouch–cleft contacts, in experiments strictly controlled in time, and analyzed these using high‐resolution imaging.ResultsPharyngeal teeth in medaka were present only when the corresponding anterior pouch had reached the ectoderm (i.e., a physical pouch–cleft contact established), similar to the situation in zebrafish. Oral teeth were present even when the treatment started approximately 4 days before normal oral tooth appearance.ConclusionsRA dependency for pharyngeal tooth formation is not different between zebrafish and medaka. We propose that the differential response to DEAB of oral versus pharyngeal teeth in medaka could be ascribed to the distinct germ layer origin of the epithelia involved in tooth formation in these two regions.