The development, homeostasis maintenance, and damage repair of the skeletal system require continuous proliferation and differentiation of stem and progenitor cells. Although studies on bone marrow mesenchymal stem cells (BMSCs) have accumulated substantial evidence over the past decades, the definition and markers of skeletal stem cells (SSCs) remain controversial. Recent advances in lineage tracing and bioinformatics technologies have facilitated the purification and functional investigation of SSCs. This review systematically summarizes different SSC populations based on their origins and markers, as well as their functions in skeletal development and repair.