SET domain-containing methyltransferases post-translationally modify a variety of cellular proteins, such as histones, cytochrome c, ribulose-bisphosphate carboxylase/oxygenase, and ribosomal proteins. In the fission yeast Schizosaccharomyces pombe, at least 13 SET domain-containing proteins have been identified in the genome, four of which are involved in transcriptional regulation through their modification of histone tails. However, the roles played by the other SET domain proteins in cellular processes and their physiological substrates remain unresolved. We show here that S. pombe Set11, a SET domain-containing protein encoded by SPCC1223.04c, specifically modifies Rpl12 (ribosomal protein L12). Recombinant Set11 prepared from Escherichia coli had catalytic activity and methylated a 17-kDa polypeptide in cellular extracts of set11 mutant cells. The methylated protein was isolated by two-dimensional gel electrophoresis or by reverse-phase chromatography and was identified as Rpl12 by mass spectrometry. In vitro methylation experiments using wild-type and mutant Rpl12 proteins verified that Set11 modified recombinant Rpl12 and suggested that its potential target site was lysine 3. The methylation site modified by Set11 was also confirmed by mass spectrometric analysis, which also revealed other unique methylation sites of Rpl12. Finally, we found that Set11 predominantly localized to the nucleolus and that the overproduction of Set11 caused a severe growth defect. These results suggest that Rpl12 methylation occurs during the ribosomal assembly processes and that control of the Set11 expression level is important for its cellular function.