This study was undertaken to characterize otic fungal flora encountered in normal dogs, atopic dogs with no clinical or cytological evidence of otitis and dogs with otitis externa. Forty-two normal dogs, 23 atopic dogs and 32 dogs with otitis were included in the study. Samples for otic fungal culture and cytology were obtained from all animals, for a total of 194 ears. Sixty-seven ear samples (34%) were culture positive for saprophytic fungal organisms, as follows: 43 (64%) Penicillium species, 13 (19%) Aspergillus species and the remaining 17% comprised of various other saprophytic fungal organisms. Cytological evidence of saprophytic fungal colonization or infection was not found in any animal. There was no relationship between positive saprophytic fungal culture and any study group. Thirty-three ear samples (17%) were positive for Malassezia pachydermatis. Cytological findings of Malassezia were significantly associated with positive culture for Malassezia (P = 0.006 left ear; P = 0.019 right ear). Furthermore, increased numbers of Malassezia led to a higher chance of positive culture (P = 0.003 left ear; P = 0.008 right ear; McNemar's test). Malassezia pachydermatis was more likely to be cultured from ears with increased cerumen. Ear type (erect or pendulous) was not significantly associated with positive culture for Malassezia or saprophytic fungal organisms. There was no relationship between positive Malassezia culture and any study group; however, Malassezia was more likely to be cultured from individual dogs in the atopic or otitis groups that also had other dermatological signs consistent with allergic dermatitis and/or pyoderma (P = 0.031 left ear; P = 0.005 right ear).