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In the nasal cavity, olfactory receptor neurons are situated in the sensory epithelium and act to transduce odor signals, whereas the respiratory epithelium is responsible for removing unwanted particles from inhaled air. Although several molecular markers have been identified to define multiple specific cell types in the sensory epithelium, less is known to indicate cells in the respiratory domain. We have recently shown that the non-visual photoreceptor opsin 3 (Opn3) is expressed in the developing olfactory region. This raised the question as to which functional role/s Opn3 might play in the nasal epithelium, as well as whether other non-visual photoreceptors may be expressed in this region. By using Opn3-eGFP and Opn5-tdTomato reporter mice in combination with Foxj1, Ker8, OMP, Sox2, and Tubb3 immunohistochemistry analyzes, our findings show that Opn3 is restricted to the olfactory sensory domain from early embryonic stages, whereas Opn5 is up-regulated in the respiratory epithelium at later developmental stages. In adulthood, Opn3 is expressed in Sox2/Ker8-positive sustentacular cells in the sensory epithelium, whereas Opn5 expression remains in the respiratory epithelium, thus indicating that these molecular markers could be used to distinguish the sensory versus respiratory epithelia. Studies of morphology and expression patterns of Foxj1, Ker8, OMP, Sox2, and Tubb3 in adult Opn3-/- and Opn5-/- mice did not reveal differences from wild-type mice. In addition, neither Opn3-/- nor Opn5-/- mice exhibited a disturbance in olfaction compared to wild-type littermates when performing a buried food test.