The present paper aims to retrospectively analyze the antimicrobial agent susceptibilities and clinical distributions of Enterococcus faecalis (E. faecalis) and E. faecium causing bloodstream infection in a tertiary hospital in Shanghai, and to lay a foundation for the clinical treatment of infections caused by these bacteria. The collected strains of E. faecalis and E. faecium were isolated between February 2012 and September 2016. The bacteria were identified by bioMérieux VITEK antimicrobial susceptibility testing system, and their clinical distribution and drug resistance were analyzed. Thirty E. faecalis and 17 E. faecium strains were obtained. E. faecalis strains were mainly from urology, gastroenterology and hematology departments, accounting for 13.33%, 16.67% and 10.00%, respectively. The resistance rates of E. faecalis to penicillin, ampicillin, ciprofloxacin, levofloxacin, tetracycline and erythromycin were 13.33%, 10.00%, 36.67%, 33.33%, 66.67% and 60.00%, respectively. The resistance rates of E. faecium to these antimicrobial agents were 88.24%, 82.35%, 88.24%, 76.47%, 23.53% and 70.59%, respectively. The resistance rates of E. faecium to penicillin, ampicillin, ciprofloxacin and levofloxacin were significantly higher than those of E. faecalis and the resistance rate to tetracycline was significantly lower than that of E. faecalis. Most of the E. faecium (29.41%) samples were from gastroenterology department. Both were sensitive to tigecycline, linezolid and vancomycin. However, the minimum inhibition concentration of vancomycin against E. faecium was significantly lower than that of E. faecalis. This study provided data support for the empirical treatment of infections caused by the two bacteria.