The organization of the amygdaloid complex in amphibians possesses major features shared with amniotes. Basic subdivisions have been identified and tentatively compared with their counterparts in other tetrapods. However, problems appeared when trying to find homologies for the amphibian vomeronasal amygdala, the medial amygdala (MeA), because of its embryological origin and, therefore, its evolutionary significance could not be established. Thus, in the present study the main characteristics of the MeA in anurans were studied during development by means of tract-tracing, immunohistochemical, and gene expression techniques. The connectivity of the MeA, mainly related to the accessory olfactory bulb and the hypothalamus, and the localization of neurochemical markers such as substance P, somatostatin, and GABA strongly support its homology with the medial amygdala (subpallial) of mammals. In addition, analysis of the expression patterns of the LIM-homeodomain genes x-Lhx5/7/9 in the developing MeA, together with the immunohistochemistry for GABA and the transcription factor NKX2.1, evidence its resemblance to the subpallial component of the vomeronasal amygdala of mammals in terms of embryological origin and, most likely, the presence of migrated cells from other territories. No evidence was found for pallial-derived territories in the vomeronasal amygdala of anurans that could be comparable to the cortical portions that exist in amniotes, suggesting that these cortical components have emerged in the anamnio-amniotic transition in the evolution of tetrapods. J. Comp. Neurol. 503:815–831, 2007. © 2007 Wiley-Liss, Inc.