Pavlovian fear conditioning is an established learning paradigm that allows to study neural mechanisms of memory formation in various species and that may be employed to emulate specific aspects of anxiety disorders. We investigated, in mice, molecular and physiological processes in the amygdalo-hippocampal system that are involved in the consolidation of such fear memory. Through gene expression analysis we identified several molecular factors (GABA synthesizing enzymes, neuropeptides, cell adhesion molecules and cytoskeleton-associated proteins) that appear to be in the experience-dependent modifications of neural activity and connectivity during this process. With the help of genetic models we were able to determine the contribution of these factors to specific aspects of fear memory storage and the related information flow in the amygdalo-hippocampal system. Thus a key role of local GABAergic interneurons has emerged, which by modifying information flow in amygdalo-hippocampal circuits critically contribute to the consolidation of specific fear memories. Molecular analysis has now led to a more precise picture of the role of specific interneuron subpopulations in, e.g., contextual and cued aspects of fear memory, and to the identification of intracellular signalling pathways that are involved in the reorganisation of such local circuit function during fear memory formation.