The pineal gland plays a central role in the photoneuroendocrine system and acts as a photosensory organ in lower vertebrates. The orphan nuclear receptor Rev-erb (NR1D1) has previously been shown to be expressed in the pineal and to be regulated with a robust circadian rhythm during zebrafish embryogenesis. This early pineal expression is under the control of the transcription factor Orthodenticle homeobox 5 (Otx5). In this paper, we show that Otx5 regulates the second zfRev-erb promoter, ZfP2. Despite the absence of a classical Otx binding site within ZfP2 this regulation depends on the integrity of the Otx5 homeodomain. Mapping experiments as well as gel shift assays (EMSA) show that this interactions between Otx5 and ZfP2 depends on a non-canonical bipartite Otx binding site (GANNCTTA and TAAA) that we called Pineal Expression Related Element (PERE). We showed that PERE is necessary for pineal expression in vivo by injecting zebrafish embryos with wild type and mutated versions of zfRev-erb promoter fused to GFP. Interestingly, PERE is found upstream of other genes expressed in the pineal gland suggesting that it may play an important role in governing pineal expression. Our data establish that PERE is a novel cis-acting element contributing to pineal-specific gene expression and to Otx target gene regulation.