Runx1 is required for the formation of hematopoietic stem cells (HSCs) during embryogenesis. The extent of developmental plasticity inherent to the HSC remains in question. We developed a system whereby the developmental fate of all Runx1-expressing cells can be traced in vivo. We present data that details the generation and initial characterization of the Runx1^IRES-Cre allele. Loss of Runx1 function in adult mice has several effects on hematopoiesis including an increase in the number of phenotypic hematopoietic stem cells (pHSCs). We utilized a congenic transplant model to demonstrate that the increase in pHSCs reflects a cell autonomous role for Runx1. By comparing gene expression profiles of wild type and Runx1-deficient pHSCs, we identified an expression signature specific to Runx1-deleted pHSCs which suggests those cells expand in number due to increased cell proliferation. We confirm this notion by demonstrating that Runx1 is required to maintain HSC quiescence. We then show that expression of the Prader-Willi Syndrome gene, Necdin (Ndn) in HSCs is Runx1-dependent, and that restoring Ndn expression in Runx1-deficient pHSCs, rescues the quiescence defect. Finally, we characterize hematopoiesis in Ndn-deficient embryos and transplant recipients of Ndn-deficient HSCs, and identify Ndn as a novel regulator of hematopoiesis.