Neurons in the pontine parabrachial nucleus (PBN) transduce signals for the general visceral sensory, somatic sensory, gustatory, and autonomic nervous systems, and the various PBN neurons that perform these functions are intermingled. In this study, we analyzed PBN gene expression profiles in male Wistar rats and obtained data on gene expression in the PBN and the principal sensory nucleus of the trigeminal nerve (Pr5). Using these data in combination with in situ hybridization analyses, we identified genes that showed higher expression in the PBN than in Pr5. Our findings indicate that expression patterns in the PBN were different for different genes: Fxyd6, syt5, and plxnc1 were expressed in many neuron populations in the PBN, while the expression patterns of calcr and asb4 were restricted to the central lateral subnucleus and waist area. Furthermore, calcr and asb4 expression patterns were distinct from those of neurotransmitters/neuropeptides such as neurotensin and calcitonin gene-related peptides. Satb2 was specifically expressed in the waist area, which is essential for gustation. In-depth analysis of spatial distribution in the PBN enabled classification of the genes into seven characteristic spatial expression patterns. Expression signatures differed significantly in the subnuclei of the rostral half, mediodorsal half, and ventrolateral third of the PBN, indicating a correlation between the spatial arrangement of the subnuclei and the molecular characteristics of the corresponding neurons. Thus, our results provide valuable information regarding the molecular features and neurotransmission mechanisms of PBN neurons that transmit specific types of information.