Multipotent embryonic cells are capable of contributing to a multitude of cell types in the body. As the development progresses, these progenitor cells become restricted in lineage competency for germ layer derivatives. At gastrulation, the pluripotent epiblast cells are allocated to the progenitors for tissues of the ectoderm, mesoderm, and endoderm[1]. However, when and whereabouts of the allocation of the progenitors and their developmental trajectory towards germ layer tissues are not well understood. Previous studies of nematode and zebrafish embryos identified a subset of progenitors that display dual propensity of differentiation to mesoderm and endoderm[2]. In this study, we identified the location of the mesendoderm progenitors in the germ layers of the mouse embryo and characterised the molecular signature of these bipotential progenitors by single-cell transcriptomic analysis. The lineage descendants of the bipotential progenitors were tracked in mouse embryos, mouse epiblast stem cells and in vitro human early embryo models. Overall, we have identified the bipotential progenitors in the in vivo setting and demonstrated their due contribution to the anterior mesendoderm, anterior definitive endoderm and cranial mesoderm of the mouse embryo. Understanding the origin, molecular signature and lineage specification of the bipotential progenitors will enable efficient generation of biologically relevant cell types for tissue engineering applications.