Histone lysine methylation is considered to be a relatively stable modification associated with important functions in epigenetic gene control and for organizing chromatin domains. Genes encoding mammalian homologues of the Drosophila suppressor of PEV Su(var)3-9 were the first shown to encode proteins with histone lysine methyl-transferase (HKMT) activity. A hallmark signature of this class of proteins is the evolutionary conserved SET-domain found in numerous chromatin regulators, and was named for its occurrence in genes encoding three such regulators in Drosophila, namely Su(var)3-9, E(z) and trithorax. Here we describe the characterization of a putative SET-domain gene in Drosophila melanogaster, G9a. The gene encodes a protein of 1637 amino acids with similar domain architecture as the mammalian homologue of same name. Whole mount in situ hybridization shows that the gene is maternal and immunostaining shows nuclear localization of DmG9a. A yeast two-hybrid screening revealed that DmG9a interacts with Tungus, a LIM-domain protein associated with α-Actinin. Further analysis is needed to investigate the functional implications of this putative interaction.