The mouse otocyst, an anlage of the inner ear, is an attractive experimental target for developing treatment modalities for congenital inner ear diseases and for studying inner ear development. Poly-arginine (6–12 residues) is a cell-penetrating peptide and can be used to deliver cargo into cells. Here, we achieved transutero delivery of enhanced green fluorescent protein (EGFP) fused to a nine-arginine peptide into mouse embryonic otocysts. The EGFP signal was detected both in the lining cells of the otocysts and in their vicinity at 18 h post injection. Mice injected with EGFP fused to a nine-arginine peptide had normal auditory and vestibular functions. These data suggest that protein transduction using poly-arginine may be a useful alternative strategy to commonly used gene delivery methods for delivering therapeutically relevant molecules to the developing inner ear.