Retinoic acid (RA), an active metabolite of vitamin A, is a crucial signaling molecule involved in tissue morphogenesis during embryonic development. RA distribution and concentration is precisely regulated during embryogenesis by balanced complementary activities of RA synthesizing (RALDH) and metabolizing (CYP26) enzymes. Here, we describe the identification of a novel murine p450 cytochrome belonging to the CYP26 family, mCYP26C1. Sequence alignment show that mCYP26C1 is more closely related to mCYP26B1 than mCYP26A1. At early developmental stages (E8.0-E8.5), mCyp26C1 is expressed in prospective rhombomeres 2 and 4, in the first branchial arch and along the lateral surface mesenchyme adjacent to the rostral hindbrain. At E9.5, mCyp26C1 expression persists in rhombomere 2 and in the maxillary and mandibular components of the first branchial arch, and is strongly induced in the lateral cervical mesenchyme. By mid-gestation, mCyp26C1 is weakly expressed in the cervical mesenchyme and in the maxillary component of the first branchial arch. At E11.5, mCyp26C1 can only be seen in a narrow band in the lateral cervical mesenchyme. During late gestation, mCyp26C1 exhibits region-specific expression in the inner ear epithelium and a persistent expression in the inner dental epithelium of the developing teeth. This pattern of expression suggests that mCYP26C1 may play an important role in protecting the hindbrain, first branchial arch, otocyst and tooth buds against RA exposure during embryonic development.