The dorsal raphe nucleus is located on the midline of the brainstem and is part of the raphe nucleus, consisting of the rostral and caudal subdivisions.

The rostral aspect of the dorsal raphe is further divided into interfascicular, ventral, ventrolateral and dorsal subnuclei. The projections of the dorsal raphe have been found to vary topographically, and thus the subnuclei differ in their projections. An increased number of cells in the lateral aspects of the dorsal raphe is characteristic of humans and other primates.