We studied the lipophilic microbiota of the external ear canals of 332 animals (264 dogs and 68 cats), with and without otitis externa, over an 11-year period from 1988 to 1999. Malassezia pachydermatis was isolated from 62.2% and 50% of dogs with and without otitis externa, respectively, and from 41.2% and 17.6% of cats with and without otitis externa, respectively. In the group of animals studied for lipid-dependent species, these yeasts were isolated from 4.5% of dogs with otitis externa and from 23.1% and 8.9% of cats with and without otitis externa, respectively. M. sympodialis and M. furfur were isolated from cats and M. furfur and M. obtusa from dogs. Our findings show that lipid-dependent Malassezia species may contribute to the etiology of otitis externa in dogs and cats.