Ectodermal contribution to the induction of pharyngeal teeth that form in the endodermal territory of the oropharyngeal cavity in some teleost fishes has been a matter of considerable debate. To determine the role of ectodermal cell signaling in scale and tooth formation and thereby to gain insights in evolutionary origin of teeth, we analyzed scales and teeth in rs-3 medaka mutants characterized by reduced scale numbers due to aberrant splicing of the ectodysplasin-A receptor (edar). Current data show that, in addition to a loss of scales (83% reduction), a drastic loss of teeth occurred in both oral (43.5% reduction) and pharyngeal (73.5% reduction) dentitions in rs-3. The remaining scales of rs-3 were irregular in shape and nearly 3 times larger in size relative to those of the wild-type. In contrast, there was no abnormality in size and shape in the remaining teeth of rs-3. In wild-type medaka embryos, there was a direct contact between the surface ectoderm and rostral endoderm in pharyngeal regions before the onset of pharyngeal tooth formation. However, there was no sign of ectodermal cell migration in the pharyngeal endoderm and hence no direct evidence of any ectodermal contribution to pharyngeal odontogenesis. These data suggest differential roles for Eda-Edar signaling in the induction and growth of scales and teeth and support the intrinsic odontogenic competence of the rostral endoderm in medaka.