The basolateral amygdala (BLA) shows firing activity synchronized with neocortex slow oscillations, a form of <1-Hz oscillations that occur dominantly during slow-wave sleep or under anesthesia and is believed to contribute to the formation of emotional memories. Despite its importance for elucidating the neural circuits involved in the formation of emotional memories, the mechanism of the synchronization has remained unclear, mainly because it is difficult to record neuronal membrane potentials in deep brain regions, such as the BLA. We recorded membrane potentials of BLA neurons using a new method that enables whole-cell recording from deep brain regions in vivo. We found that BLA neurons transiently depolarized at late active phases in the slow oscillations. To determine the neural source of the depolarization of BLA neuros, we focused on the medial prefrontal cortex, whose axons projecting to the BLA is known to contribute to the formation of fear memories, as a candidate region that depolarizes BLA neurons during slow oscillations. BLA-projecting neurons were retrogradely labeled with channelrhodopsin-2 using retrograde adeno associated virus, and their firing activity was recorded using an opto-tagging method. These results provide insight into the neural mechanism that synchronizes the slow oscillations between the BLA and the neocortex and lead to the elucidation of the mechanism underlying the formation of emotional memories.