Neuroanatomical concepts of the hypothalamus, the forebrain territory that controls homeostasis and drives in vertebrates, are over 100 years old. Neuroanatomists of the 19th century generally considered the hypothalamus to consist of the tuberal or infundibular area, a median prominence at the brain ventral surface at the location of the pituitary gland, framed in front and at the sides by the optic chiasm and tracts. The neural plate fate maps of amniotes and anamniotes are strictly comparable from a topological point of view. The relative positions of the prospective brain areas can be extrapolated from one species to another. The prospective longitudinal or axial dimension of the brain is best represented by the neural/non-neural border of the neural plate, which will transform into the longitudinal roof plate of the closed neural tube. This developmental analysis suggests that all adult median forebrain derivatives found between the anterior commissure and the mamillary area are equally rostralmost loci in the brain. At the open neural plate, the rostral forebrain primordium contains the prospective hypothalamus as a large area centered upon the alar, basal, and floor portions of the terminal wall, its caudal part covering as well a rostral part of the lateral wall, whereas the prospective telencephalon forms a thin band at the dorsal periphery of the alar portion of these domains, including the corresponding roof area. A handful of genes, coding either for transcription factors or secreted protein morphogens, participate in early patterning and regional identity specification along the AP and DV dimensions of the whole forebrain, including the hypothalamus. The complex networked interplay of many molecular signals that control brain development represents a dynamic ontogenetic system that tends to reach different equilibrium states in different parts of the neuroepithelial wall.