The dorsal raphe nucleus (DRN) through its extensive efferent projections has been implicated in a great variety of physiological and behavioral functions including the regulation of the sleep-wake cycle. This nucleus is composed of five sub-regions defined according to the distribution of its serotonergic (5-HT) neurons. In addition to its heterogeneity in neuronal populations, the DRN contains a great diversity of 5-HT neuronal subtypes identified based on their electrophysiological characteristics, morphology and sub-regional distribution. This suggests that the DRN sub-regions may play different functional roles. Recent studies reported long-range inputs specific to the 5-HT neurons of the DRN; but they did not differentiate whether some inputs were specific to a DRN sub-region, or another region. To fulfill this gap, we have previously described the forebrain afferents to the different sub-regions of the DRN using cholera toxin b subunit and Phaseolus vulgaris-leucoagglutinin, as retrograde and anterograde tracers respectively. In the present work, we provide a detailed map of the brainstem projections to these different sub-regions. We show that if some brainstem structures project homogeneously to all sub-regions, most of the brainstem long-range inputs project in a topographically organized manner onto the DRN and, moreover, that a rich interconnected network is present within the DRN.