[Objective] To find out the antibiotic resistance of 15 (1 β-lactam and 14 non-β-lactams) antibiotics and potential antibiotic resistance genes of Enterococcus faecalis, isolated from natural fermented food.[Methods] The antibiotic resistance of Enterococcus faecalis was detected with 15 antibiotics by micro broth dilution method. Then the genome-wide association study was applied to find the potential antibiotic resistance genes of Enterococcus faecalis by Scoary. [Results] This study showed that the 16 strains of Enterococcus faecalis were 100% sensitive to kanamycin, vancomycin, linezolid and erythromycin, but 100% resistant to clindamycin. In addition, the different degrees of antibiotic resistance to other antibiotics were showed in Enterococcus faecalis. The genome-wide association study found 9 potential antibiotic resistance genes, which were significantly correlated with 5 antibiotics (chloramphenicol, ciprofloxacin, trimethoprim, neomycin and tetracycline). Genes, including FAM000296 and FAM005768, were related to the resistance of chloramphenicol, trimethoprim and ciprofloxacin. FAM000296 and FAM005768 were both annotated as SecG, while compared to FAM000296, FAM005768 lost 21 bases at the 3 end. [Conclusion] Enterococcus faecalis isolated from natural fermented products is resistant to many antibiotics and carries potentially antibiotic resistant genes in its genome. Therefore, a comprehensive safety of Enterococcus faecalis should be assessed before application.