Despite their indisputable efficacy for pain management, opiates prescription remains highly controversial due to their elevated addictive potential. Relapse in drug use is one of the principal problems for addiction treatment, being drug-associated memories among its main triggers. Consequently, the extinction of these memories has been proposed as a useful therapeutic tool. Hence, by using the conditioned place aversion (CPA) paradigm in rats we investigated some of the molecular mechanisms that occurred during the retrieval and extinction of morphine withdrawal memories in the basolateral amygdala (BLA) and the hippocampal dentate gyrus (DG), which control emotional and episodic memories, respectively. The retrieval of aversive memories associated with the abstinence syndrome paralleled with decreased mTOR activity and increased Arc and GluN1 expressions in the DG. Additionally, Arc mRNA levels in this nucleus very strongly correlated with the CPA score exhibited by the opiate-treated rats. On the other hand, despite the unaltered mTOR phosphorylation Arc augmented in the BLA. After the extinction test, Arc and GluN1 expressions raised in both the DG and BLA of control and morphine-treated animals. Remarkably, Homer1 expression in both areas correlated almost perfectly with the extinction showed by morphine-dependent animals. Also, Arc expression in the DG correlated strongly with the extinction of the CPA manifested by the group treated with the opiate. Finally, our results support coordinated activity of some of these neuroplastic proteins for the extinction of morphine activity in a regional-dependent manner. Present data provide evidence of differential expression and activity of synaptic molecules during the retrieval and extinction of aversive memories of opiate withdrawal in amygdalar and hippocampal regions that will likely permit the development of therapeutic strategies able to minimize relapses induced by drug-associated aversive memories.