The nucleus reuniens (RE) is part of the midline thalamus and one of the major sources of thalamic inputs to the hippocampal formation and the medial prefrontal cortex. However, it not only sends strong efferents to these areas but is also heavily innervated by both brain regions. Based on its connectivity and supported by functional studies the RE has been suggested to represent a major hub in reciprocal hippocampal–prefrontal communication. Indeed, inactivation studies have demonstrated that this nucleus is particularly important for cognitive behaviors which depend on prefrontal–hippocampal communication, such as working memory or memory consolidation. However, besides its central role in mediating hippocampal–prefrontal communication, the RE is target of a multitude of other cortical and subcortical afferents, which likely modulate its function. So far, however, studies that have systematically investigated the afferents of the RE have only been performed in rats. Because of the unique role of the mouse as a genetically accessible model system for mammalian brain circuit analysis we have mapped the afferent connectivity of the mouse RE using retrograde Fluoro‐Gold tracing. Comparison with similar data from rats indicated a very high level of similarity in prefrontal and hippocampal afferents but some differences in afferent connectivity with other brain regions. In particular, our results suggest interspecies differences regarding the integration of the RE in circuits of fear, aversion, and defense.