The mammary epithelial system is a heterogeneous cellular compartment thought to be comprised of two major cell types, basal and luminal respectively, that are in flux throughout an individual’s life and require a stem cell compartment to maintain. Questions remain about the origin and nature of these stem cells, and how the constituent components of the gland interplay in order to maintain a healthy tissue or ultimately responds to cancer present. Through the usage of single cell microfluidic based experimental tools, we have been able to explore this relevant heterogeneity with single cell RNA sequencing (scRNA-seq) in human and mouse and single cell ATAC sequencing (scATAC-seq) in mouse. We highlight in both species the different basal and luminal cell types, with the stratification of the luminal compartment into hormone response or secretory cells. Additional relevant cell states present within the secretory luminal cell type manifest with tissue relevant consequences. Using scRNA-seq in human we present three major epithelial cell types, one basal and two distinct luminal referred to as L1 (Secretory) and L2 (Hormone Responsive). After applying pseudotemporal reconstruction, it is shown that the three populations interconnect in a developmental lineage with basal cells branching into the two luminal end points. In mouse, a similar three epithelial cell type structure is highlighted in the mammary gland with both scRNA-seq and scATAC-seq in an integrated analysis. The secretory luminal compartment is additionally stratified into luminal progenitor and lactation-committed progenitors, with distinct regulatory features underpinning each cell state through both cis and trans acting elements. Taken together, these results emphasize newly discovered heterogeneity in the luminal compartment of the mammary gland, challenging of previously held definitions of the mammary stem cell, and the underlying regulation of cell state.