This report investigates in what way functional connectivity may explain how two memory systems that share almost all their structures, can function as separate systems. The first series of experiments was aimed at demonstrating the reliability of our experimental design by showing that acquisition of the spatial version of a water cross-maze task (stimulus-stimulus associations) was impaired by dorsal hippocampal lesions whereas the cue version (stimulus-reinforcement association) was altered by amygdala lesion. Then, we evaluated how these two tasks induce different patterns of connectivity. The connectivity was evaluated by calculating the correlations between the zif-268 immunoreactivity of 22 structures composing the hippocampus and the amygdala systems. We designed a new statistical procedure to demonstrate double dissociations on the basis of brain regional intercorrelations. Our data show that the correlations between the hippocampus and the other structures of the memory system are higher in the place-learning group compared to the cue-learning group, whereas they are enhanced with the amygdala in the latter group compared to the former. This demonstrates that the activation of a memory system consists in the focusing of functional connectivity toward the central structure of the system. This may explain how several memory systems can share the same structures while remaining independent.