Metallothionein (MT) is a small cysteine-rich metal-binding protein involved in metal homeostasis and protection against heavy metal and oxidative stress. MT is abundant in the central nervous system, but its function is not well known. We cloned two MT genes (mt2 and smtb) in the zebrafish (Danio rerio) and examined their localization in the brain to predict potential function of MT in the adult zebrafish brain. Comparison of genomic sequences of mt2 genes showed conserved synteny between the mammals and teleosts. However, smtb gene could be a zebrafish species specific isoform, as there are no similar genes identified in other teleosts and vertebrates. Zebrafish MT genes expression were seen in the brain, eye, gill, heart, liver, muscle, ovary and testis. In the brain, in situ hybridization showed the expression of mt2 in the pia mater, surrounding the ventricles, ventral nucleus of ventral telencephalic area, dorsal zone of the periventricular hypothalamus, periventricular gray zone of the optic tectum, nucleus of medial longitudinal fascicle, central gray, ventral rhombencephalic commissure, and the cerebellar corpus, most of which are cell proliferating regions. Similarly, smtb is also expressed in cell proliferating regions. Double-labeling with neuronal (HuC/D) and glial (glial fibrillary acidic protein, GFAP) markers showed that both mt2 and smtb are expressed in neurons but not in glial cells. The localization patterns of mt2 and smtb suggest their possible role in neural cell proliferation in the brain of adult zebrafish.