More than 160 distinct RNA modifications have been discovered to date. Recent technical advances have enabled the precise detection of several RNA modifications and their transcriptome-wide distribution, new functions and players in mRNA. These efforts leads to the discovery of RNA modifications associated with hitherto unknown gene regulatory mechanisms, resulting in the birth of the epitranscriptomics field that deciphers the function of RNA modifications. N6-methyladenosine (m6A) represents the most prevalent internal modification on mRNA. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m6A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m6A modifications. We further demonstrate that FIP37 mediates m6A on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m6A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants. Future work will focus on exploring the mechanisms underlying biological and genetic effects of plant epitranscriptome, and defining a conceptual framework for the regulatory roles of RNA modifications in plants.