The amygdala complex is a diverse group of more than thirteen nuclei, segregated in five major groups: the basolateral (BLA), central (CeA), medial (MeA), cortical (CoA) and basomedial (BMA) amygdala nuclei. These nuclei can be distinguished depending on their cytoarchitectonic properties, connectivity, genetic and molecular identity, and most importantly, on their functional role in animal behavior. The extended amygdala includes the CeA, as well as the bed nucleus of the stria terminalis (BNST). Both CeA and the BNST share similar cellular organization, including common neuron types, reciprocal connectivity, and many overlapping downstream targets. In this section, we describe the advances of our knowledge on neuronal diversity in the amygdala complex and BNST, based on recent functional studies, performed at genetic, molecular, physiological and anatomical levels in rodent models, especially rats and mice. Molecular and connection property can be used separately, or in combinations, to define neuronal populations, leading to a multiplexed neuronal diversity supporting different functional roles.