<span class="paragraphSection"><div class="boxTitle">Abstract</div><span style="font-style: italic;">N</span>⁶-methyladenosine (m⁶A) and <span style="font-style: italic;">N</span>⁶, 2′-O-dimethyladenosine (m⁶Am) are two RNA modifications that play essential roles in diverse RNA metabolic processes and functions. Despite their importance, the dynamic landscapes and regulatory patterns of m⁶A and m⁶Am during the oocyte-to-embryo transition (OET) in humans and mice remain elusive. Here, we developed a highly sensitive method, MeLACE-seq, to profile the m⁶A and m⁶Am landscapes across human and mouse oocytes to pre-implantation embryos. We reveal that the zygotic genome activation (ZGA) stage serves as a regulatory node where both the m⁶A and m⁶Am methylomes undergo dramatic, species-specific changes. Moreover, transcripts marked by m⁶A and m⁶Am are generally expressed and translated at higher levels than unmarked transcripts. Additionally, we discovered that m⁶A modifications are extensively deposited on human retrotransposon RNAs. These m⁶A marks exhibit a functional shift, showing a positive correlation with elevated retrotransposon RNA levels in pre-ZGA embryos, but a negative correlation with their expression around the ZGA stage. Together, these findings reveal conserved and species-specific regulatory patterns of the epitranscriptome during human and mouse OETs, providing new insights into the roles of RNA modifications in embryogenesis.</span>