Melanin synthesis in the hair follicle (HF) is strictly coupled to the growth stage of the hair cycle and is interrupted during follicle regression (catagen) and resting. Using tyrosine-related protein 2 (Trp)2-LacZ transgenic mice as a model, we show that distinct melanocyte subpopulations of the HF display distinct patterns of apoptosis and survival during catagen. Melanocytes located in the outer root sheath express Bcl-2 and are TUNEL-negative. Part of the pigment-producing melanocytes located above the follicular papilla expresses Fas, TUNEL, and is likely to undergo apoptosis, whereas the other part of these melanocytes expresses c-kit, Bcl-2, and becomes visible in the follicular papilla. During late catagen, TUNEL and Ki-67 negative melanocytes expressing Bcl-2 are seen in the secondary germ of the HF. Lack of proliferation in the follicular melanocytes during catagen suggests that secondary hair germ of late catagen HF is most likely repopulated by melanocytes arising from the outer root sheath or follicular papilla of early/mid-catagen HF. Taken together, these data suggest a possible scenario and mechanisms of the remodeling of the follicular pigmentary unit during HF anagen-catagen-telogen transition and may be used for the establishing in vivo models for pharmacological modulation of melanocyte apoptosis and survival during the hair cycle.