Distinct aspects of our fearful experiences appear to be mediated by separate explicit and implicit memory processes. To identify brain regions that support these separate memory processes, we measured contingency awareness, conditional fear expression, and functional magnetic resonance imaging signal during a Pavlovian fear conditioning procedure in which tones that predicted an aversive event were presented at supra and sub-threshold volumes. Contingency awareness developed in conjunction with learning-related hippocampal and parahippocampal activity on perceived conditioning trials only. In contrast, conditional fear and differential amygdala activity developed on both perceived and unperceived trials, regardless of whether contingency awareness was expressed. These findings demonstrate the distinct roles of these brain regions in explicit and implicit fear memory processes.