The composition of the skin microbiome varies widely among individuals sampled at the same body site. A key question is which molecular factors determine strain-level variability within sub-ecosystems of the skin. We used a genomics-guided approach to identify an antibacterial biosynthetic gene cluster inCutibacterium acnes(formerlyPropionibacterium acnes) that is widely distributed across individuals and skin sites. Experimental characterization of this cluster enabled the identification of a new thiopeptide antibiotic, cutimycin. Analysis of individual human skin hair follicles showed that cutimycin is an important factor regulating colonization resistance againstStaphylococcusspecies.One Sentence SummaryCutimycin, a thiopeptide antibiotic produced by a widespread skin commensal, reducesStaphylococcuscolonization of human follicles.