The pineal gland, or epiphysis, sits on the roof of the diencephalon and is a simple photoreceptive structure in most anamniotes that acquired aneuroendocrine role in mammals. Its structure is comparable to the primitive eye found in mollusk or ascidians. Our fate map of the anterior neural plate, in zebrafish, localized the pineal precursors in a very lateral position, coinciding with the pre-placodal territory. Genetic loss of function studies further show that the formation of the epiphysis requires Dlx3, a protein strictly expressed in placodal ectoderm. Mis-expression experiments demonstrate that the combinatorial expression of the homeodomain transcription factors Dlx3 and Flh/Noto is sufficient to confer pineal identity. Finally, observations made in otx1;otx2 double loss of function embryos reveal that pineal cell fate specification, controlled by Dlx3 and Noto, occurs during gastrulation and is negatively regulated by the Fgf signaling pathway. All together, our study uncovers the placodal nature of the pineal complex and identifies the genetic trigger of its specification during late gastrulation. Implications on evolution of the anterior neural ectoderm will be discussed.