During gastrulation, mammalian embryos generate three germ layers from the epiblast: ectoderm, mesoderm and endoderm. We studied the epigenetic landscape of single epiblast cells, which revealed lineage priming towards the three germ layers. Within the epiblast cells with mesodermal priming, a subset shows a strong signature for the endothelial fate. Through clonal analysis and live imaging, we show that the embryonic endothelium is a distinct population from the rest of mesodermal derivatives. Accordingly, we found early onset of endocardial cell differentiation during mesoderm migration. These results show silent epigenetic priming of endothelial precursors in the epiblast, and suggest they remain on-hold for differentiation to allow gastrulation followed by immediate differentiation.