Epitranscriptome refers to any relevant changes in gene expression without changes in RNA sequences. Similar to epigenetic changes, the epitranscriptomic changes are in general mediated by post-transcriptional chemical modifications of RNA species. Recently, mRNA modifications, especially both N6-methyladenosine (m6A) and N1-methyladenosine (m1A), have received significant attention as proteins responsible for generating, removing or recognizing m6A modification have been identified. m6A in eukaryotic cells including human and mouse was initially identified in early 1970s. However, the function of the modification has not been intensively studied because of technical limitations. Recently, using next-generation sequencing (NGS) technology, several groups revealed transcriptome-wide distribution of m6A and its both in vitro and in vivo roles in biological processes such as metabolism and development. The review focuses on recent progress in mRNA modification and stem cell biology. In addition, an integrated landscape of m6A enrichments in both human and mouse embryonic stem cells (ESCs) is presented using publically available datasets.