M.EcoGII is the only known bacterial methyltransferase that catalyzes non-site-specific N6-adenine methylation on both DNA and RNA. Although the enzyme could be used to manipulate RNA methylation states, the activity of RNA methylation is much less than that of DNA methylation. Here, we performed ancestral sequence reconstruction to improve the RNA methylation activity of M.EcoGII. Five ancestors of M.EcoGII were selected from a maximum-likelihood phylogeny for ancestral sequence reconstruction. These ancestral enzymes were expressed in E. coli, purified, and characterized. In vitro methylation assays showed that all ancestors had a higher activity for RNA than M.EcoGII, with Anc284 showing 12 times higher RNA methylation activity. Multiple sequence alignment indicated the 14 amino acid residues in charge of substrate specificity. The RNA-selective M.EcoGII ancestor would be applicable to the epigenetic tools for manipulating RNA methylation states