Otitis externa is an inflammation of the epithelium lining the ear canal and is one of the most common diseases that affect dogs and cats, affecting about 5-20% of dog population and 2-6% of cats. Because of the relevance of the subject and the frequency of cases observed in clinical medicine, this study aimed to perform a survey of the main isolated microorganisms associated with its resistance profile. This study was conducted through otologic swabs of dogs and cats, received for analysis from August 2004 to December 2015, in Microbiological Animal Diagnostic Center at Santa Catarina State University (UDESC). The samples came from Veterinary Clinic Hospital at UDESC and private veterinary clinics in the city of Lages-SC. A total of 234 otologic swabs were received during the period, 222 (94.9%) from dogs and 12 (5.1%) from cats. 234 samples were analyzed and 182 (77.7%) showed bacterial growth with ten different genus of bacteria isolated. The most isolated species were Staphylococcus pseudintermedius (50 - 27.4%), followed by coagulase-negative Staphylococcus (41 - 22.5%) and Pseudomonas aeruginosa (21 - 11.5%). It was used several antimicrobials in antibiogram test according to their availability, the most used were fluoroquinolones group, and enrofloxacin was resistant in 20.9% (30) of isolates and norfloxacin in 24.1% (142). In the beta-lactam class, penicillin had a higher resistance profile with 56.6% (73/129) followed by ampicillin with 46.7% (57/122). The gentamicin and neomycin are the main antibiotics used in cases of otitis externa and obtained low resistance rates, 17.6% (22/125) and 19.23% (20/124), respectively. Another widely used antibiotic is tobramycin which showed 33.3% of resistance, but it was used in a few tests only (5/15). Therefore, the major bacterial genus isolated in cases of otitis externa in dogs and cats was Staphylococcus, although some strains have shown a high degree of resistance against certain antibiotics, the most used clinically still have a good efficacy in treating the disease.