Acne vulgaris (AV) has been associated with Cutibacterium acnes (C. acnes) colonization in sebaceous follicles. However, recent studies have revealed the role of skin microbiome dysbiosis in acne pathogenesis. AV grading, which is classified by the sum of noninflammatory and inflammatory lesions, is essential in making clinical decisions about AV management. Henceforth, a better understanding of the skin microorganism profile in AV is needed. Our purpose was to compare microbiome profiles between different grades of AV severity. The microbiome samples were collected by swabbing from 108 participants with various AV grades in accordance with the classification from Lehmann. The V3-V4 regions of the 16 S rRNA gene were sequenced and analysed. The difference in the percentage of C. acnes among different grades of AV severity was not significant. However, the proportion of Staphylococcus epidermidis (S. epidermidis) was significantly greater in severe AV than in mild AV (0,3 vs. 0,1%; p = 0,046). The difference in the Shannon index between the groups was not remarkable. Several skin commensals were also found in the samples. However, only the proportion of Staphylococcus caprae (S. caprae) was significantly greater in mild AV than in moderate and severe AV (1.5% vs. 0.7% vs. 1.1%, p = 0.004). These results indicate that the degree of AV severity may be distinguished from the degree of dysbiosis associated with changes in skin commensal microorganisms, specifically S. epidermidis and S. caprae. This study was registered at ClinicalTrials.gov on April 28, 2023, under registration number NCT05838534. © The Author(s) 2024.