SummaryAiming to unravel the top of the mammary epithelial cell hierarchy, a subset of the CD49fhighCD24med mammary repopulating units (MRUs) was identified by flow cytometry, expressing high levels of CD200 and its receptor CD200R1. These MRUCD200/CD200R1 repopulated a larger area of de-epithelized mammary fat pads than the rest of the MRUs, termed MRUnot CD200/CD200R1. MRUCD200/CD200R1 maintained a much lower number of divergently defined, highly expressed genes and pathways that support better cell growth, development, differentiation, and progenitor activity than their MRUnot CD200/CD200R1 counterparts. A defined profile of hierarchically associated genes supporting a single-lineage hypothesis was confirmed by in vitro mammosphere analysis that assembled 114 genes with decreased expression from MRUCD200/CD200R1 via MRUnot CD200/CD200R1 toward CD200+CD200R1− and CD200R1+CD200− cells. About 40% of these genes were shared by a previously published database of upregulated genes in mammary/breast stem cells and may represent the core genes involved in mammary stemness.