The pilosebaceous unit (PSU) is composed of multiple compartments and the self-renewal of PSU depends on distinct hair follicle stem cell (HFSC) populations. However, the differential roles of the HFSCs in sebaceous gland (SG) renewal have not been completely understood. Here, we performed multiple lineage tracing analysis to unveil the contribution of different HFSC populations to PSU regeneration during the hair cycle and wound healing. Our results indicated that the upper bulge stem cells contributed extensively to the SG replenishment during hair cycling, while HFSCs in the lower bugle did not. During skin wound healing, all HFSC populations participated in the SG replenishment. Moreover, β-catenin activation promoted the contribution of HFSCs to SG replenishment, whereas β-catenin deletion substantially repressed the event. Thus, our findings indicated that HFSCs contributed to SG replenishment in a β-catenin-dependent manner.