N-6-methyladenosine (m(6)A) has been identified as the most abundant modification on eukaryote messenger RNA (mRNA)(1). Although the rapid development of high-throughput sequencing technologies has enabled insight into the biological functions of m(6)A modification(2-13), the function of m(6)A during vertebrate embryogenesis remains poorly understood. Here we show that m(6)A determines cell fate during the endothelial-to-haematopoietic transition (EHT) to specify the earliest haematopoietic stem/progenitor cells (HSPCs) during zebrafish embryogenesis. m(6)A-specific methylated RNA immunoprecipitation combined with high-throughput sequencing (MeRIP-seq) and m(6)A individual-nucleotide-resolution cross-linking and immunoprecipitation with sequencing (miCLIP-seq) analyses reveal conserved features on zebrafish m(6)A methylome and preferential distribution of m(6)A peaks near the stop codon with a consensus RRACH motif. In mettl3-deficient embryos, levels of m(6)A are significantly decreased and emergence of HSPCs is blocked. Mechanistically, we identify that the delayed YTHDF2-mediated mRNA decay of the arterial endothelial genes notch1a and rhoca contributes to this deleterious effect. The continuous activation of Notch signalling in arterial endothelial cells of mettl3-deficient embryos blocks EHT, thereby repressing the generation of the earliest HSPCs. Furthermore, knockdown of Mettl3 in mice confers a similar phenotype. Collectively, our findings demonstrate the critical function of m(6)A modification in the fate determination of HSPCs during vertebrate embryogenesis.