Hematopoietic stem cells (HSCs) are important in cell-based therapies for blood-related disorders. While progress has been made in generating HSCs by directed differentiation of pluripotent stem cells (PSCs), such cultures promote hematopoietic progenitor cells (HPCs) over HSCs. Thus, elucidating markers and factors associated with HSC versus HPC development is imperative. HSCs and HPCs originate from hemogenic endothelium (HE) in a Runx1-dependent process. Here, we characterize a Runx1 enhancer (+110) that distinguishes emerging dorsal aorta HSCs from HPCs. Comparative transcriptomics reveal a 17-gene signature associated with in vivo long-term HSC potential, while single-cell multiome analysis demonstrates a clear epigenetic identity of dorsal aorta HE, preHSCs, and HPCs, providing a resource of stage-specific enhancer activity. Our study demonstrates the power of cell type-specific enhancer-reporter models to dissect cell fate decisions in development and provides new inroads to label and/or perturb HSC versus HPC potential in vivo and in vitro.