Post-translational modifications of histones have been demonstrated to play important roles in the regulation of chromatin structure and transcriptional regulation. In histone modification, methylated lysine has an important role in transcriptional regulation. The evolutionarily conserved SET domain was first identified in Drosophila proteins: Suppressor of variegation (Su(var)3-9), Enhancer of zeste (E(z)), and Trithorax. SET domain-containing proteins have histone methyltransferase (HMTase) activity via the SET domain. Using a bioinformatics approach, we identified and cloned zebrafish setd3 containing SET and Rubis-subs-bind domains. In this study, we report that setd3 had lysine specificity toward histone H3K36. Methylation of histone H3K36 is known as one of the transcriptional activation markers. It transiently transfected setd3 activated general transcription in reporter assays. Overexpression of setd3 decreased cell viability and activated caspase-3, indicating possible roles in apoptotic cell death and cell cycle regulation.