The hypothalamus is a phylogenetically ancient brain region vital for the regulation of sleep, hunger, thirst, sexual behavior, and thermoregulation. Structurally in mammals, the hypothalamus is subdivided into a dozen morphologically and molecularly distinct nuclei that subserve unique functions. In lower vertebrates these nuclei are less defined, although imprecise clusters of the same neuronal phenotypes are observed. Despite its physiological importance, how hypothalamic neurons are specified, differentiate, and migrate during development is only beginning to be understood. Indeed, while layer formation (e.g. cortex) has been well studied, comparatively little is known about the molecular mechanisms that guide the movement of neurons into nuclei. One reason for this disparity is the assumption that neuronal clusters lack a precise organization. This is mistaken – on the contrary, most brain nuclei exhibit an impressive suborganization – thereby making examination of hypothalamic development feasible.  In this presentation, I will discuss molecular mechanisms that regulate specific patterns of progenitor cell proliferation and fate specification as well as neuronal differentiation and migration. In particular, I will focus on similarities of this program across species, starting with zebrafish and moving to mice and humans. I will end my presentation with a discussion about mechanisms that might drive the coalescing of hypothalamic neurons into distinct nuclear structures.