Innate behaviors in mammals are mediated by a connected circuit of limbic system structures, which most prominently includes the olfactory system, bed nucleus of stria terminalis (BNST), medial amygdala (MeA) and hypothalamus. Our previous work (Hirata et al., Nature Neuroscience, 2009; Carney et al., Neural Development, 2010) revealed that Dbx1+ progenitors derived from a specialized progenitor niche generate an electrophysiologically homogeneous subpopulation of MeA inhibitory projection neurons that are distinct from their non-Dbx1 derived populations. Here, we reveal that in the MeA, Dbx1 -derived neurons possess a unique molecular profile of expression of behaviorally relevant genes and in a sexually dimorphic manner. Consistent with this, Dbx1 and non-Dbx1 MeA projection neurons appear to have biases in the processing of specific aspects of innate information. Thus, it appears that subpopulations of MeA neurons that can be divided according to expression of developmentally regulated and/or functionally relevant genes are dedicated to processing different aspects of innate information.