ObjectivesTo evaluate evidence of Malassezia overgrowth following successful topical antibacterial monotherapy of refractory canine bacterial otitis using semi‐quantitative cultures.Materials and MethodsTwenty‐nine dogs with bacterial otitis were treated topically with either fluoro‐quinolone [0.5% enrofloxacin (18 dogs, 19 treatment events, 25 ears) or 0.1% marbofloxacin (1 ear), with 0.1% dexamethasone] (“FQ”) SID, or 143 mg/mL piperacillin/18 mg/mL tazobactam (“PT”) BID (11 dogs, 14 treatment events, 19 ears) for 8 to 36 days (mean 20 days). At visits 1 (V1) and 2 (V2), ear swab tips were washed in PBS + Triton X‐100 and serial dilutions spread‐plated onto blood, MacConkey (37°C, 48 hours) and modified Dixon's agar (32°C, 14 days) to generate semiquantitative counts. Microbes were identified by phenotype and MALDI‐TOF.ResultsPrior to treatment, Pseudomonas aeruginosa was isolated alone or in combination with other bacteria in 14 FQ‐treated ears and 18 PT‐treated ears; the next most frequent bacteria were Streptococcus canis (8 FQ, 2 PT) and Staphylococcus pseudintermedius (8 FQ, 1 PT). The proportions of dogs' ears (excluding cross‐over treatments and contra‐lateral affected ears) from which bacteria were isolated were significantly reduced by treatment with both FQ (V1, 13/15; V2, 5/15) and PT (V1, 14/14; V2, 2/14). The proportions of dogs' ears from which yeasts (Malassezia pachydermatis, Candida spp.) were isolated were significantly increased by treatment in dogs treated with PT (V1, 1/14; V2, 14/14) but not FQ (V1, 3/15; V2, 6/15).Clinical SignificanceOtitis cases that receive potent antibacterial monotherapy must be monitored for yeast overgrowth.