Indicator bacteria reflect the overall microbiological hygiene status in the food industry. Enterococcus species, particularly E. faecalis and E. faecium, are representative hygiene indicators; however, other species have not been thoroughly evaluated for their role as indicators. In the present study, we compared the isolation rates between E. faecalis/faecium (EF) and non-faecalis/faecium Enterococcus spp. (NFE) in dairy foods and characterized them to evaluate their applicability as alternative hygiene indicators with the prevalence. A total of 39 Enterococcus spp. isolates consisting of 10 EF (25.6%, 9 E. faecalis and E. faecium) and 29 NFE (74.4%, 11 E. durans, 3 E. gallinarum, and 15 E. hirae) were isolated from 75 dairy samples in a farmstead cheesehouse in South Korea. Biochemical diversities among isolates demonstrated that various isolates were contaminated at each cheesemaking step. Thirty-four out of 39 isolates exhibited antibiotic resistance to at least one antibiotic and 4 NFE isolates harbored at least one virulence gene. In conclusion, despite their scarce evidence of virulence, NFE may be alternative hygiene indicators given their high prevalence in dairy samples. •Prevalence of non-faecalis and non-faecium Enterococcus species was higher.•E. durans was predominant in dairy food.•Non-faecalis and non-faecium Enterococcus species had antibiotic resistance.•Virulence and antibiotic resistance genes were identified.