The mammalian habenula is involved in regulating the activities of serotonergic and dopaminergic neurons. It consists of the medial and lateral habenulae, with each subregion having distinct neural connectivity. Despite the functional significance, manipulating neural activity in a subset of habenular pathways remains difficult because of the poor availability of molecular markers that delineate the subnuclear structures. Thus, we examined the molecular nature of neurons in the habenular subnuclei by analyzing the gene expressions of neurotransmitter markers. The results showed that different subregions of the medial habenula (MHb) use different combinations of neurotransmitter systems and could be categorized as either exclusively glutamatergic (superior part of MHb), both substance P-ergic and glutamatergic (dorsal region of central part of MHb), or both cholinergic and glutamatergic (inferior part, ventral region of central part, and lateral part of MHb). The superior part of the MHb strongly expressed interleukin-18 and was innervated by noradrenergic fibers. In contrast, the inferior part, ventral region of the central part, and lateral part of the MHb were peculiar in that acetylcholine and glutamate were cotransmitted from the axonal terminals. In contrast, neurons in the lateral habenula (LHb) were almost uniformly glutamatergic. Finally, the expressions of Htr2c and Drd2 seemed complementary in the medial LHb division, whereas they coincided in the lateral division, suggesting that the medial and lateral divisions of LHb show strong heterogeneity with respect to monoamine receptor expression. These analyses clarify molecular differences between subnuclei in the mammalian habenula that support their respective functional implications.