Microbiological examinations are frequently performed as part of breeding management examinations in the bitch, but also in case of (suspected) reproductive tract problems. As most bacteria are opportunistic pathogens, evaluation of bacterial findings is challenging for veterinarians. Besides, breeders might request antimicrobial treatment in breeding bitches, fearing conception failure—even without medical indication. Considering the rising threat of antimicrobial resistance, gaining deeper insights into the bacterial findings from the vagina of healthy and (suspected) reproductive-diseased bitches might contribute to the knowledge of the canine aerobic vaginal flora and consequently improve the responsible use of antibiotics. We analyzed results from bacteriological cultures of 23,254 vaginal swabs sent in to three commercial laboratories in Germany between 2015 and 2021, where standard aerobic microbiological examination was carried out. We found a variety of 319 bacterial species that mostly grew in mixed cultures of two or more bacterial species. Commonly found species were Escherichia coli, beta-hemolytic Streptococci, coagulase-positive Staphylococci, Pasteurellales, and aerobic sporulators, as well as other Streptococcus spp. Our results showed a large diversity of the canine vaginal flora in healthy and (suspected) reproductive-diseased bitches. They largely support earlier findings of small studies on the physiological canine vaginal flora, emphasizing that solely the results of a bacterial evaluation should not be the base for antimicrobial treatment. Instead, bacterial findings should be evaluated with the results of a clinical gynecological examination.