In Pavlovian fear conditioning, an aversive unconditional stimulus (UCS) is repeatedly paired with a neutral conditional stimulus (CS). As a consequence, the subject begins to show conditional responses (CRs) to the CS that indicate expectation and fear. There are currently two general models competing to explain the role of subjective awareness in fear conditioning. Proponents of the single-process model assert that a single propositional learning process mediates CR expression and UCS expectancy. Proponents of a dual-process model assert that these behavioral responses are expressions of two independent learning processes. We used backward masking to block perception of our visual CSs and measured the effect of this training on subsequent unmasked performance. In two separate experiments we show a dissociation between CR expression and UCS expectancy following differential delay conditioning with masked CSs. In Experiment 1, we show that masked training facilitates CR expression when the same CSs are presented during a subsequent unmasked reacquisition task. In Experiment II we show that masked training retards learning when the CS+ is presented as part of a compound CS during a subsequent unmasked blocking task. Our results suggest that multiple memory systems operate in a parallel, independent manner to encode emotional memories.