Occurrence of Malassezia, mites and bacteria, was evaluated through cytology, culture and microscopical analysis of auricular cerumen collected from 115 cats and 203 dogs with otitis externa. For the dentification of Malassezia species, a PCR-based technique was also used. All the patients enrolled in the study were examined for Malassezia and all cats and 101 dogs were also investigated for mites. Bacteriological examination was performed on 16 cats and 60 dogs. The associations between Malassezia and the other pathogens and the correlations between Malassezia and season, gender and ear conformation, were evaluated. Malassezia pachydermatis was isolated from 58.2% cats and 52.7% dogs, while Otodectes cynotis was identified in 66.1% cats and in 5.9% dogs. Bacteria were detected in 18.7% cats and 36.7% dogs and Staphylococcus pseudointermedius, Staphylococcus epidermidis, Pseudomonas aeruginosa, Streptococcus canis, Escherichia coli and Bacillus sp. were identified. M. pachydermatis was isolated in pure culture from 28.3% cats and from 87.1% dogs, while it was associated with O. cynotis in 70.1% of cats and in 5% of dogs, and with bacteria in 1.5% of cats and 23.3% of dogs. Mixed infections caused by M. pachydermatis, bacteria (S. pseudointermedius) and mites occurred in 1 cat and 1 dog. Our results suggest that ear conformation is an important individual predisposing factor for Malassezia otitis in dogs and indicated the influence of the season on onset of Malassezia infections in cats