The roles of orexin and histamine in regulation of sleep and wakefulness in rodents appear complementary. Both are also involved in regulation of feeding, histamine through both H1 and H3 receptors. Zebrafish offers a possibility to study the interactions of these systems both morphologically on systems level and behaviorally. We studied the networks of histaminergic and orexinergic systems in zebrafish using in situ hybridization and immunohistochemistry, and functions of these systems with translation inhibition using morpholino-oligonucleotides and suicide inhibitor of histidine decarboxylase alfa-fluoromethylhistidine. The singly orexinergic diencephalic cell group was efficiently connected to all major aminergic systems in the zebrafish brain. The histaminergic system, consisiting of a single posterior diencephalic cell cluster, sent distinct descending fiber systems to the hindbrain, and the optic tectum was innervated in a laminar manner by histamine-containing nerve fibers. The densest histaminergic projections were found in the dorsal telencephalon, and area which also showed highest expression of both H1 and H3 receptors. Translation inhibition of histidine decarboxylase with morpholino oligonucleotides induced a strong reduction in histamine content, which lasted for almost two weeks. This effect was associated with decreased locomotion during the light phase, suggesting that histamine in zebrafish is involved in activity regulation during the light period. Lack of histamine also induced a clear alteration in the dark-induced startle. These effects were partly resotored by administration of H1 receptor agonists. These results suggest that histamine and orexin systems in zebrafish resemble those found in mammals. Histamine is involved in activity regulation through at least H1 receptor, most likely through a telencephalic mechanism.