The current study aimed to assess the prevalence of Enterococcus species isolated from some farmed fish species, including tilapia (Oreochromis niloticus), brush tooth lizard (Saurida undosquamis), horse mackerel (Trachurus trachurus), and red porgy (Pagrus pagrus) sold in Zagazig city, Sharkia Governorate, Egypt. Additionally, antimicrobial susceptibility testing was performed for Enterococcus species using the disc diffusion method. Furthermore, multiplex PCR was performed to identify virulence-associated genes of Enterococcus faecalis isolates. The results indicated contamination of the examined fish with various Enterococcus species with an overall total prevalence of 52.5%. The identified Enterococcus species were E. faecalis (26.25%), E. faecium (15%), and E. hirae, E. raffinosus, and E. durans (3.75%, each). The antibiotic sensitivity test revealed variable resistance patterns of the retrieved isolates to various antimicrobial agents, such as kanamycin (100%), clindamycin (76.9%), sulfamethoxazole (69.2%), ampicillin (69.2%), and colistin (61.5%). PCR screening of virulence genes revealed that E. faecalis harbored sodA (100%), gelE (83.3%), and ace (50%) genes. Consequently, urgent measures are needed to implement hygienic practices to control microbial contamination in both the aquatic environment and fish markets