This study was to compare and assess the accuracy of species-level identification methods for Enterococcus spp., and to understand the species distribution and antimicrobial susceptibility characteristics of Enterococcus spp. collected of raw pork from a free trade market in Beijing. Methods By using matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS)and 16S rRNA gene analysis, the species of Enterococcus spp. were identified, and the inconsistent results were further identified by API 20 Strep, 16S rRNA and 23S rRNA gene analysis. Moreover, the susceptibility of isolated Enterococcus spp. to 10 antibiotics was analyzed at species level. Results Among the five identification methods, 16S rRNA gene analysis showed 100.0% consistence with the final species identification results, but the VITEK 2 COMPACT showed the lowest consistence of only 4.0%(1/25). The most prevalent species in Enterococcus spp. was Enterococcus faecalis, accounting for 82.6% (71/86) followed by Enterococcus hirae 14.0% (12/86). Enterococcus faecalis strains showed higher antimicrobial susceptibility than Enterococcus hirae to ciprofloxacin, tetracycline, high-level streptomycin and high-level gentamicin (ciprofloxacin: χ²=10.751, P<0.01; tetracycline:χ²=3.865, P>0.05; high-level streptomycin:χ²=1.608, P>0.05; high-level gentamicin:χ²=0.553, P>0.05), but showed apparently lower antimicrobial susceptibility on erythromycin and chloramphenicol than Enterococcus hirae (erythromycin:χ²=20.244, P<0.01; chloramphenicol:χ²=14.139, P<0.01). Conclusion The 16S rRNA gene analysis and MALDI-TOF-MS have higher accuracy at species level identification for Enterococcus spp.. Different species of Enterococcus spp. showed various antimicrobial susceptibility characteristics. This study was important for the effective monitoring of drug-resistant enterococci spread and prevalence.