Propionibacterium acnes, a gram-positive, anaerobic, and aerotolerant bacterium that is found frequently in the skin as part of the human microbiome causes inflammatory acne, shoulder infection, and the contamination of medical devices. The study goals were the antibiotic resistant and molecular epidemiological characterization of the P. acnes isolates in Korea. A total of 22 P. acnes isolates originated from diverse patients were obtained from three National Culture Collections for Pathogens in South Korea. The hemolytic properties and minimum inhibitory concentrations (MIC) of five antibiotics (tetracycline, doxycycline, clindamycin, erythromycin, and minocycline) were determined. Only one isolate showed high MIC values and resistance to all five antibiotics. Genotypic characterization was achieved by multilocus sequence typing (MLST) for eight loci (aroE, guaA, tly, camp2, atpD, gmk, lepA, and sodA) and repetitive-sequence-based PCR (rep-PCR) analysis using the DiversiLab kit. MLST revealed four phylogroups that were type IA₁ (27.3%), type IA₂ (18.2%), type IB (13.6%), and type II (40.9%). Rep-PCR results demonstrated three clusters that were cluster I (39.1%), cluster II (45.5%), and cluster III (13.6%). The isolates of cluster I were part of phylogroup type IA (both IA₁ and IA₂), and the isolates of cluster II belonged to phylogroup type II. All isolates of phylogroup type IB were hemolytic and belonged to cluster III. The results of rep-PCR clustering analysis showed a good correlation with those of MLST phylogroups, suggesting that rep-PCR could be an alternative method to track P. acnes subtype lineages.