The mammary gland is composed of two distinct epithelial cell lineages that expand during puberty to form a network of branching and budding ducts. During pregnancy further branching and proliferation drives the formation of secretory lobuloalveolar structures, a process that is repeated in successive reproductive cycles. The unique capacity of the postnatal mammary epithelium to undergo extensive proliferation and regeneration is attributed to the existence of adult mammary stem cells (MaSCs). Whilst recent genetic fate mapping studies using lineage-specific promoters have provided valuable insight into the developmental fate of adult MaSCs, the hierarchical organisation of mammary epithelial cells and the molecular identity of MaSCs remain equivocal. We have utilised a random mutation-induced genetic labelling strategy to indelibly mark a single mouse MaSC and its progeny in situ. Combined with optical tissue clearing and 3D confocal imaging, individual clones arising from a single parent cell can be visualised in their entirety, revealing their contribution to ductal and alveolar morphogenesis. Our findings highlight the limitations of using lineage-specific promoters to mark putative MaSCs and reveal valuable new insights into the mammary epithelial cell hierarchy.