RING finger protein38 (rnf38) is highly expressed in the brain. However its function remains to be elucidated. In the present study, full length sequence of medaka (Oryzias latipes) rnf38 mRNA and the relationship between the rnf38 and the serotonergic system in the medaka brain were analysed. Full length medaka rnf38 cDNA consisted of 2726 nucleic acids spanning 12 exons and the deduced protein sequence consisted of 518 amino acid residues including a RING finger domain, a KIT motif and a coiled-coil domain. Medaka were exposed to citalopram (CIT), and their behaviour and gene expressions of pet1, solute carrier family 6, member 4A (slc6a4), tryptophan hydroxylase (tph2) and rnf38 in the brain were examined. Medaka exposed to CIT exhibited anxiety-like behaviour. The pet1, slc6a4 and tph2 gene expressions were significantly lower in the hindbrain and the rnf38 gene was significantly higher in the telencephalon and the hypothalamus exposed to CIT. This suggests that rnf38 expression is modulated by the serotonergic system.