Background: With the extensive use of oral antibiotics for treatment of moderate to severe acne, it is important to understand the association of such antibiotic use with changes not only in Cutibacterium acnes (C. acnes) but also in the complete bacterial community of the skin. Objectives: We sought to investigate the changes of skin microbiota in acne patients in association with oral antibiotics. Methods: The skin microbiota of acne patients, before and after taking 6 weeks of oral antibiotics (oral doxycycline, 100mg, twice daily) were compared. Skin areas on the cheek were sampled for 16S ribosomal RNA gene sequencing. Results: Twenty patients were included in this study (11 female, 8 males, ages between 11-44 years). Across all patients, antibiotic treatment was associated with reduction in the levels of C. acnes, Snodgrassella alvi, Corynebacterium matruchotii etc., and an increase in Neisseria oralis, Enterococcus hirae et al. There also was a significant change in microbial diversity represented by Shannon and Inverse Simpson index. Conclusion: In this study, oral antibiotic treatment of acne was associated with changes in the composition and diversity of the skin microbiota.