Merkel cells are specialized cells in the skin that are important for proper neural encoding of light touch stimuli. Conflicting evidence suggests that these cells are lineally descended from either the skin or the neural crest. To address this question, we used epidermal (Krt14^Cre) and neural crest (Wnt1^Cre) Cre-driver lines to conditionally delete Atoh1 specifically from the skin or neural crest lineages, respectively, of mice. Deletion of Atoh1 from the skin lineage resulted in loss of Merkel cells from all regions of the skin, while deletion from the neural crest lineage had no effect on this cell population. Thus, mammalian Merkel cells are derived from the skin lineage.