In eukaryotes, changes in chromatin structure regulate the access of gene regulatory sequences to the transcriptional machinery and play important roles in the repression of transposable elements, thereby protecting genome integrity. Chromatin dynamics and gene expression states are highly correlated, with DNA methylation and histone post-translational modifications playing important roles in the establishment or maintenance of chromatin states in plants. Histones can be covalently modified in a variety of ways, thereby affecting nucleosome spacing and/or higher-order nucleosome interactions directly or via the recruitment of histone-binding proteins. An extremely important group of chromatin modifying enzymes are the histone lysine methyltransferases (HKMTs). These enzymes are involved in the establishment and/or maintenance of euchromatic or heterochromatic states of active or transcriptionally repressed sequences, respectively. The vast majority of HKMTs possess a SET domain named for the three Drosophila proteins that are the founding members of the family: Suppressor of variegation, Enhancer of zeste and Trithorax. It is the SET domain that is responsible for HKMT enzymatic activity. Mutation of Arabidopsis HKMT genes can result in phenotypic abnormalities due to the improper regulation of important developmental genes. Here, we review the different classes of HKMTs present in the model plant Arabidopsis thaliana and discuss what is known about their biochemical and biological functions.