Background: Precise roles of P. acnes and other anaerobic bacteria in the acne pathogenesis are still unclear. Recent studies have shown that P. acnes can be further classified into several phylotypes with distinct phenotypes and virulences. Objectives: We analyzed distribution patterns of P. acnes and Peptostreptococcus phylotypes from acne patients and healthy control. Methods: A total of 370 samples from 95 acne patients and 65 samples from 65 healthy controls were investigated. Each phylotype was identified by PCR methods using type-specific primers. Results: There was no significant difference in the microflora of the skin surface from acne and healthy controls. In acne lesions, distribution patterns between surface and comedonal lesions were not different, while they were significantly different from those of both papules and pustules. In the inflammatory lesions, the proportion of type IA P. acnes was increased, while those of type IB and II were decreased. The proportion of Peptostreptococcus species was also increased in the inflammatory lesions. Parallel distribution patterns were observed as the disease severity aggravated. There was no significant difference in sebum output between patients infected with type IA and those with type IB or II. Conclusion: Our results suggest that surface microflora at the phylotype levels might not be important in triggering acne and type IA P. acnes and Peptostreptococcus species might be more closely associated with inflammatory acne lesions.