In facial seborrheic dermatitis (SD), lower fungal diversity was evident accompanied by increased relative abundances of Malassezia and Staphylococcus and reduced relative abundance of Cutibacterium. Topical ketoconazole treatment led to Malassezia reduction and increase in fungal diversity to restore skin microbial communities.

• Before and after topical ketoconazole treatment, cutaneous microbial communities of SD were characterized by employing a high-throughput DNA sequencing method in this prospective cohort study including 30 patients with facial SD and 15 age- and gender-matched healthy controls.

• Lesional sites of facial SD had significantly lower bacterial and fungal diversities, vs controls.

• Facial SD demonstrated decreased relative abundance of Cutibacterium and increased abundances of Malassezia and Staphylococcus.

• Disease diversity was found to be positively correlated with the relative abundances of Malassezia, Staphylococcus and Corynebacterium.

• Post-ketoconazole use, significant increase in fungal Shannon diversity and the relative abundances of Candida and Aspergillus was seen at the lesional sites, and the relative abundance of Malassezia exhibited a decreasing trend.

• Until 2 weeks post-treatment, these changing trends were maintained.