Endometritis is an important cause of subfertility with high economic impact in mares and is mostly associated with bacterial infections. The aim of this study was to investigate bacterial pathogens in uteri and the susceptibility of some clinical isolates against several antimicrobial agents frequently used to control bacterial endometritis in mares in Germany. A total of 247 uterine swabs taken from mares with fertility problems were cultured to isolate bacteria and in vitro antimicrobial susceptibility of beta-hemolytic Streptococcus spp. and Escherichia coli (E. coli) strains was determined. Totally, 151 samples (61.1%) were found culture positive. A total of 332 microorganisms including 331 bacteria and one fungus were isolated from the samples. From the bacteria, 21,9%, 15.9%, 15.4%, 12%, 10.5%, 5.7% and 3.0% of the isolates were identified as Escherichia coli (E. coli), alpha- hemolytic streptococci, beta-hemolytic streptococci, Bacillus spp., gamma-hemolytic streptococci, coliform bacteria and Staphylococcus aureus (Staph. aureus) respectively. The remaining isolates (15.6%) included 13 other bacterial species and one fungus. beta-hemolytic streptococci and E. coli strains were considered as frequently associated with fertility problems and antimicrobial susceptibility of these isolates against 14 antimicrobial agents including penicillin, tulathromycin, tetracycline, erythromycin, florfenicol, ceftiofur, amoxicillin, amoxicillin/clavulanic acid, enrofloxacin, gentamicin, cefquinome, colistin, marbofloxacin and sulfamethoxazole/trimethoprim was determined. All beta-hemolytic streptococci were found to be susceptible to penicillin, ceftiofur, amoxicillin/clavulanic acid, enrofloxacin, cefquinome, marbofloxacin and sulfamethoxazole/trimethoprim, whereas 29.3% of beta-hemolytic streptococci showed resistance against colistin. All E. coli strains and 50% of them were resistant to penicillin and erythromycin, respectively, wheres all E. coli isolates were sensitive to all other tested antimicrobial agents used in this study.