The isolation of genes influencing long-term memory is critical for an understanding of learning at the molecular level. Recently, chromosomal substitution rat strains, known as consomics, have been developed. Here we report the results of the first study on aversive learning and memory with these consomic rats. We compared the Fawn Hooded Hypertensive (FHH) and Brown Norway (BN) parent strains with a Brown Norway chromosome 1 substitution on the FHH background (FHH-1(BN)). Results indicated that while all strains had normal short-term memory, the FHH animals were impaired relative to BN in tests of long-term memory for a discrete auditory cue. This deficit was rescued by the introgression of the BN1 chromosome onto the FHH background. Furthermore, the FHH-1(BN) consomic showed an enhancement in long-term contextual fear memory relative to the FHH strain. These changes were not due to differences in pain sensitivity as both strains performed equally on two different pain tests. These results provide preliminary support that consomic rat strains can be a useful tool in identifying genes related to long-term fear memory formation.