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Although hypothalamus is a brain region of utmost importance for its role in the neuronal and hormonal control of key homeostatic and vegetative functions, its embryological origin and anatomical definition remains imprecise. In addition, recent data comparing neuroendocrine regions in several model organisms, from protostomes to vertebrates, also point to some heterogeneity in the ancestral form these systems. To gain insight into the evolution of neuroendocrine regions of the vertebrate brain, we have compared the embryonic development of the basal forebrain in protochordates, the closest relatives to vertebrates and in a few model vertebrates (zebrafish, chicken and mouse). The complex morphogenesis of the ventral forebrain was first analyzed in 3D over time in zebrafish embryos, combining visualization of proliferation and differentiation markers, with that of regionalized developmental genes. We found that the region containing preoptic area behaves as a coherent morphogenetic entity, organized around the optic recess and located between telencephalon and hypothalamus. We named this domain “optic recess region” (ORR) as clearly distinct from hypothalamus proper, although it includes several important neuroendocrine cell populations (dopamine, vasopressin and oxytocin neurons for example). We proposed, based on embryological evidences, that this ORR of teleosts has counterpart in all the other vertebrate species, including amphibian and amniotes. Moreover, this partition of neuroendocrine regions between ORR and hypothalamus is likely to correspond to the apical and blastoporal partition of the Bilaterian forebrain proposed by D. Arendt and others. This renewed view of the morphogenesis of the forebrain also led to solve some inconsistencies in the inconsistencies in the comparison among vertebrates and in the interpretation of genetic mutations found in human and other mammals.