Exercise influences epigenetic regulation of gene expression by modulating tissue methyltransferase activity, whereas effects on methyltransferases with other crucial biological functions have not been elucidated. We performed RNA sequencing of skeletal muscle (SkM) and white adipose tissue (WAT) obtained from 26 sedentary men undergoing acute exercise (AE) and a long-term, 12-week exercise intervention (LTE). We investigated exercise effects on tissue methyltransferase transcripts and a plasma marker of methylation capacity (methionine/homocysteine ratio). Blood and tissue samples were obtained before, just after and 2 h after AE (blood and SkM), and before and after LTE (blood, SkM, WAT). Differential expression analyses revealed that 43 (15 up; 26 down) and 55 (31 up; 23 down) methyltransferases were differentially expressed in SkM just after and 2 h after AE, respectively. After LTE, 69 methyltransferases (13 up; 55 down) were differentially expressed in SkM. Upregulated methyltransferases were implicated in histone and peptidyl-lysine methylation (AE, 0 h), RNA processing (AE, 2 h), and cell communication (LTE). Downregulated methyltransferases were implicated in gene expression (AE, 0 h) and mRNA processing (LTE). Plasma methionine/homocysteine decreased after AE, but was elevated after LTE. In conclusion, AE and LTE influence SkM but not WAT methyltransferase transcript levels and plasma methionine/homocysteine.