Depression and anxiety disorders are among the leading causes of morbidity, mortality, and disability in the United States. Impaired serotonin neurotransmission appears to be a central mechanism inducing depressive and anxiety symptoms. Most serotonergic innervation of the forebrain arises from the median raphe nucleus (MRN) and dorsal raphe nucleus (DRN). The DRN displays a complex internal morphology, with distinct subregions varying across the anteroposterior (A-P) axis. However, many studies have considered the DRN as a whole or used easily confused terminology to describe position. Given the large differences in receptor expression, electrophysiological properties, and connectivity between various subregions of the DRN, it appears probable that they have distinct functional roles in the regulation of behavior. To foster uniform definitions of locations within these nuclei, we have quantitatively mapped gene expression in DRN and MRN for tryptophan hydroxylase-2 (Tph2), the serotonin transporter, as well as 5-HT1A and 5-HT1B receptors. These quantitative studies revealed differences in the density of expression of each gene in the ventromedial, dorsomedial, and dorsolateral subnuclei of the DRN, as well as distinct variation in expression across the A-P axis. These findings provide additional evidence that subregions of the DRN are heterogeneous and need to be considered independently. In addition, a fine scale map of Tph2 expression suggests definitions for categorical divisions of the DRN across the A-P axis. These are based on distinct morphological patterns of Tph2 expression and may be more reflective of physiology than the classic terminology dividing the DRN into equal thirds. J. Comp. Neurol. 498:611–623, 2006. © 2006 Wiley-Liss, Inc.