Folliculitis decalvans (FD) is an inflammatory cicatricial alopecia. Its aetiology remains unclear but an imbalance of skin microbiota seems to play a special role in the pathogenesis. The normal subepidermal microbiota resides in hair follicles and protects from opportunistic infections. Previously Staphylococcus aureus (S. aureus) was postulated to play the main role in the pathogenesis of the disease, but recent findings show it is rather opportunistic than a specific pathogen in FD. Staphylococcus aureus colonizing FD does not seem to be more virulent than one isolated from the general population, however, only a partial response to standard anti-staphylococcal antibiotic treatment suggests rather gram-negative aetiology. Antibiotic therapy may prove effective to reduce bacterial load below the threshold that triggers the immune system, but the microbiota found in FD after antibiotic treatment is not entirely restored to normal. Unbalanced microbiota with the reservoir of commensal and opportunistic bacteria in hair follicles may stoke unspecific responses of the immune system, therefore causing chronic inflammation.