Enterococci cause infections with various localizations, the most common being urinary infections. The purpose of the study was to identify the profile of the antimicrobial resistance of enterococci species (AMRE) isolated from patients hospitalized in three hospitals in Romania. We evaluated AMRE retrospectively (2019–2021) in various biological samples. The microbiological diagnosis was sustained by classical methods of bacteria culture and automatic identification. The sensitivity testing was performed by the Kirby–Bauer method, and the antibiotic minimum inhibitory concentration was tested by the automated Vitek system. We analyzed 86 strains of Enterococcus spp., identifying the following species: 47.7% E. faecalis, 47.7% E. faecium, 3.55% E. gallinarum, and 1% E. hirae. Most of the bacterial strains were isolated from urocultures (38.4%) and hemocultures (32.6%). Overall, the rate of vancomycin resistance was 5.8% for E. faecalis and 15.1%. for E. faecium. The prevalence of multidrug-resistant (MDR) strains was found to be 100% in E. gallinarum, 75.6% in E. faecium, and 21.9% in E. faecalis. The results confirm the high level of AMRE, which creates difficulties with adequate antibiotic prescriptions. The continuous monitoring of AMRE is essential for updating the local diagnostic and treatment protocols for enterococcal infections.