Swabs collected from the external ears of 942 cattle, including both European and zebu breeds, were used to evaluate the epidemiology of Malassezia species. High numbers of Malassezia isolates were significantly associated with maturity of the animals and with diagnosed otitis. In healthy animals, a particularly low prevalence of the genus was found in Holstein cows, especially in the summer months, a finding perhaps correlating with the open, air-exposed ears of this breed. Pendutlous-eared zebu breeds and hybrids had higher levels of colonization, although this effect was more pronounced in humid regions, and was least in the dry north and west of the state. The most common species seen was M. sympodialis, which accounted for 47.1% of isolates from healthy cattle and 39.1% from cattle with otitis. In cattle with otitis sampled in summer, we found that the relatively thermotolerant M. sympodialis made up 80.8% of isolates. By contrast, during the winter the less thermotolerant M. globosa was the most common species from otitis, making up 56% of the isolates. Humidity and temperature may be the main factors explaining the epidemiology of Malassezia diseases and colonizations in both animals and humans.