The aim of this case was to describe very rare infection of canine prostate gland with Stenotrophomonas maltophilia which had influence on male fertility. The bacterium was cultured from third fraction of the ejaculate collected by manual manipulation. The sperm concentration and motility parameters were evaluated by Hamilton-Thorne Sperm Analyser, version IVOS 12.3, sperm morphology by Diff-Quick staining and live/dead spermatozoa by eosin/nigrosin staining. After 3 weeks of treatment with targeted antibiotic, ciprofloxacin, there was no bacterial growth in prostate fluid. Semen parameters were improved after 60 days from the end of treatment, and females were successfully mated.