Biomedicinally important histone lysine methyltransferases (KMTs) transfer a methyl group from S-adenosylmethionine to lysine residues in histones and other proteins. Here, we report comparative studies on epigenetic methylation of lysine and γ-thialysine, the simplest cysteine-derived lysine analog, which can be introduced to histone peptides and histone proteins via site-specific bioconjugation-based cysteine alkylation. Enzyme assays and computational studies demonstrate that human KMTs catalyze efficient methylation of histones that possess γ-thialysine. This work provides a molecular basis for the application of γ-thialysine for biomolecular studies of intact histones and the nucleosome assembly.