Objective This study was to understand the structure characteristics of prophages in the genome of Enterococcus hirae R17, and also to analyze their interaction relationships with the host bacterium. Methods The gene distribution and gene encoding characteristics of prophages in the genome of Enterococcus hirae R17 were identified using the PHAST software. The virulence gene, antimicrobial resistance genes, and environmental resistance genes in the prophages were also analyzed. Results Three prophages were found on the chromosome of Enterococcus hirae,including two incomplete prophage elements (Prophage-1 and Prophage-2) and one complete prophage(Prophage-3). Some function genes of bacteria were found in the sequence of three prophages, including nucleotide transportation and metabolism related genes. One incomplete prophage carrying erythromycin- and bacitracin-resistance genes was identified in the plasmid, which suggested that prophage induced gene horizontal transfer caused erythromycin- and bacitracin-resistance of Enterococcus hirae R17. Conclusion This study laid a solid foundation for the diversity analysis of prophages of Enterococcus hirae. Prophages played an important role in promotion of antimicrobial resistance of enterococci. Scientists should pay more attention to the spread of antimicrobial resistance and pathogenicity induced by prophages.