Acne vulgaris is the most common skin diseases that people experience during their lives. Thirteen rhizosphere isolates were screened against Propionibacterium acnes. The bacterium exhibited the highest activity against P. acnes was identified as Bacillus methylotrophicus YML008 by 16S rRNA gene sequencing. Scanning electron microscopy was used to assess the changes in morphology of P. acnes. Preliminary studies on the antimicrobial substance demonstrated the hydrophilic nature of compound with MIC of 0.17mg/ml and MBC of 0.3mg/ml. The cytotoxic effect of the extract was least (80% survival) as compared to benzyperoxide (40% survival). These results suggest YML008 as a promising bioresource and may be useful as a lead bacterium to develop a new type of anti-acne skin care prep to cure or prevent acne. Further, mechanism of action and proper clinical trials may be promising for this research.