The habenulo-interpeduncular pathway, a highly conserved cholinergic system, has emerged as a valuable model to study leftright asymmetry in the brain. In larval zebrafish, the bilaterally paired dorsal habenular nuclei (dHb) exhibit prominent left-right differences in their organization, gene expression, and connectivity, but their cholinergic nature was unclear. Through the discovery of a duplicated cholinergic gene locus, we now show that choline acetyltransferase and vesicular acetylcholine transporter homologs are preferentially expressed in the right dHb of larval zebrafish. Genes encoding the nicotinic acetylcholine receptor subunits α2 and β4 are transcribed in the target interpeduncular nucleus (IPN), suggesting that the asymmetrical cholinergic pathway is functional. To confirm this, we activated channelrhodopsin-2 specifically in the larval dHb and performed whole-cell patchclamp recording of IPN neurons. The response to optogenetic or electrical stimulation of the right dHb consisted of an initial fast glutamatergic excitatory postsynaptic current followed by a slowrising cholinergic current. In adult zebrafish, the dHb are divided into discrete cholinergic and peptidergic subnuclei that differ in size between the left and right sides of the brain. After exposing adults to nicotine, fos expression was activated in subregions of the IPN enriched for specific nicotinic acetylcholine receptor subunits. Our studies of the newly identified cholinergic gene locus resolve the neurotransmitter identity of the zebrafish habenular nuclei and reveal functional asymmetry in a major cholinergic neuromodulatory pathway of the vertebrate brain.ateralization of brain function is found throughout the animal kingdom, yet knowledge of the underlying neural bases for left-right (L-R) specializations is limited. Multiple developmental mechanisms could account for differential neural activity, including asymmetry in cell number or density, in specification of neuronal types, or in connectivity. Increasing evidence suggests that L-R differences in neurotransmitter distribution also play an important role in lateralized behaviors.The bilaterally paired habenular nuclei (Hb) of zebrafish provide a valuable model to study brain asymmetry. In larvae, the dorsal habenulae (dHb) [equivalent to medial habenular nuclei (mHb) of mammals] exhibit pronounced L-R differences in size, molecular properties, and connections with their midbrain target, the interpeduncular nucleus (IPN) (1-3). The Hb-IPN pathway connects limbic areas of the forebrain and midbrain (4), and has been implicated in nicotine addiction in mammals (5).The mHb-IPN tract is a major cholinergic system across vertebrates (6-11); however, it is still unresolved whether this pathway is cholinergic in zebrafish. Cholinergic neurons are defined by the presence of choline acetyltransferase (ChAT), which synthesizes ACh from choline and acetyl CoA, and vesicular acetylcholine transporter (VAChT), which packages ACh into synaptic vesicles. The chat and vacht genes are situa...