Hippocampal networks required for associative memory formation are involved in cue- and context-dependent threat conditioning. The hippocampus is functionally heterogeneous at its dorsal and ventral poles, and recent investigations have focused on the specific roles required from each sub-region for associative conditioning. Cumulative evidence suggests that contextual and emotional information is processed by the dorsal and ventral hippocampus, respectively. However, it is not well understood how these two divisions engage in threat conditioning with cues of different sensory modalities. Here, we compare the involvement of the dorsal and ventral hippocampus in two types of threat conditioning: olfactory and auditory. Our results suggest that the dorsal hippocampus encodes contextual information and is activated upon recall of an olfactory threat memory only if contextual cues are relevant to the threat. Overnight habituation to the context eliminates dorsal hippocampal activation, implying that this area does not directly support cue-dependent threat conditioning. The ventral hippocampus is activated upon recall of olfactory, but not auditory, threat memory regardless of habituation duration. Concurrent activation of the piriform cortex is consistent with its direct connection with the ventral hippocampus. Together, our study suggests a unique role of the ventral hippocampus in olfactory threat conditioning.