The regeneration of oral maxillofacial hard tissues is currently one of the issues of most concern in public health. This complex process involves a variety of cell types residing in a specialised microenvironment known as the adult stem cell niche in living organisms. Within this niche, adult stem cells are considered to play a central role in the regeneration of hard tissues, which undergo rapid proliferation and differentiation into progenitor cells to replace lost tissue, throughout postnatal life. Their fate is tightly regulated by the niche factors secreted by the non-stem niche cells present within the same microenvironment. Over the past decades, the advent of lineage tracing techniques has revolutionised the in vivo study of cell dynamics. Through tissue- and temporally-specific labelling of Cre-expressing cells, this method enables researchers to depict the defined cell fates and differentiation trajectories. The present review summarises the progress made in lineage tracing studies of hard tissue formation cell populations residing in the oral and maxillofacial regions, with a focus on stem cells, progenitor cells and niche cells. The aim is to provide new clues for future research endeavours.