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Background: Numerous factors, such as Enterococcus antimicrobial resistance and expression of virulence factors, may account for the maintenance and prevalence of Enterococci infection. The aim of the present study was to assess the occurrence of esp and eep genes in the E.faecalis and E.facium strains isolated from the patients with urethral system infections. Materials and Methods: In this experimental study, 214 clinical samples, including 80 catheters and 134 urine samples, were collected from the patients. The identification of the isolated samples was based on the growth on Bilesculin agar culture media, tolerance of 6.5% Nacl, gram staining, and catalase, hydrolysis of hyporate, telorite reduction, arginine hydrolization, and fermentation of the carbohydrates tests. The assessment of genes was done by PCR method. Results: esp gene was present in 83% of the urine samples and in 97% of the catheters while eep gene was present in 100% of the urine samples and 90% of the urine catheters. The results of antibiogram indicated that the multi-antibiotic resistance was about 78.1% against vancomycin and tetracyclin, 75% against cyprofeloxin and tetracyclin, 59.3% against vancomycin and cyprofeloxin, and about 53% against vancomycin and streptomycin. Conclusion: The findings of this study indicate that esp gene plays an important role in formation of biofilm in patients. Due to the presence of eep gene in almost all of the samples, it can used as a rapid identical agent for the assessment of pheromone production and provision of suitable conditions for plasmid transformation between clinical strains and the prevalence of antibiotic resistance.