Protein methylation modification is one of the ways of post-translational modification. In fungi, a variety of lysine methyltransferases perform methylation of lysines at specific sites on histones. The methylation of lysine on histones is related to fungal DNA replication, transcription, and heterochromatin formation. Methylation is involved in a variety of biological processes, such as fungal development, circadian rhythm regulation, secondary metabolic gene cluster expression, hydrolase synthesis, and pathogenic fungal virulence formation. We summarize the nomenclature, classification, domains, structures of the catalytic domain of KMTs, and the roles of methylation in different fungi. We also discuss the research limitations and the future research direction.