In tetrapods, the medial amygdala is a forebrain center that integrates olfactory and/or vomeronasal signals with the endocrine and autonomic systems, playing a key role in different social behaviors. The vomeronasal system has undergone important changes during evolution, which may be behind some interspecies differences in chemosensory-mediated social behavior. These evolutionary changes are associated with variations in vomeronasal-recipient brain structures, including the medial amygdala. Herein, we employed an evolutionary developmental biology approach for trying to understand the function and evolution of the medial amygdala. For that purpose, we reviewed published data on fate mapping in mouse, and the expression of orthologous developmental regulatory genes (Nkx2.1, Lhx6, Shh, Tbr1, Lhx9, Lhx5, Otp, and Pax6) in embryos of mouse, chicken, emydid turtles, and a pipid frog. We also analyzed novel data on Lhx9 and Otp in a lacertid lizard. Based on distinct embryonic origin and genetic profile, at least five neuronal subpopulations exist in the medial amygdala of rodents, expressing either Nkx2.1/Lhx6, Shh, Lhx9, Otp/Lhx5, or Pax6. Each neuronal subpopulation appears involved in different functional pathways. For example, Lhx6 cells are specifically activated by sex pheromones and project to preoptic and hypothalamic centers involved in reproduction. Based on data in nonmammals, at least three of these neuronal subtypes might have been present in the medial amygdala of the amniote common ancestor. During mammalian evolution, the downregulation of Nkx2.1 in the alar hypothalamus may have been a driving force for an increment of the Otp/Lhx5 subpopulation.