The spontaneously hypertensive rat (SHR) is used as an animal model of attention deficit hyperactivity disorder (ADHD). It displays deficits in frontostriatal functioning, but it is unclear if medial temporal lobe functioning and structure are affected. We used behavioral tasks that evaluate functioning of the amygdala and hippocampus to compare male SHR to male rats from two inbred comparator strains, the normotensive Wistar-Kyoto (WKY) and the hypertensive Wistar-Kyoto (WKHT) rat (n = 8/strain). The three strains showed similar levels of amygdala-related stimulus-reward learning during conditioned cue preference testing. In the ambiguous T-maze task, which dissociates between spatial and habit learning, significantly more WKHT than SHR or WKY used a response (indicative of habit learning) versus a place (indicative of spatial learning) strategy during an early probe test on day 8. During a later probe test on day 24, WKY progressed significantly from using a place strategy to a response strategy. Throughout all probe tests, a place strategy was used predominately by SHR and a response strategy by WKHT. Thus, SHR exhibited deficits in dorsal striatum-related habit learning, whereas WKHT exhibited deficits in hippocampus-related spatial learning. Following behavioral testing, fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging scans were conducted in subgroups of rats from each strain (n = 4/strain). FLAIR imaging detected bilateral hippocampal hyperintensities in three of four WKHT and unilateral hippocampal atrophy in one of four SHR. The association between response strategy use during the initial probe test to forage for food in the ambiguous T-maze task and bilateral hippocampal abnormalities was significant. Collectively, while medial temporal lobe functioning appears to be normal in SHR exhibiting an ADHD-like phenotype, WKHT rats display both hippocampal functioning deficits and signs of bilateral hippocampal cell loss. The latter characteristics might be used to develop a new animal model of age- or disease-related decline in hippocampal functioning.