We previously reported that the Malassezia microbiota of the external auditory canal were composed principally of Malassezia slooffiae and Malassezia restricta. In the present study, the fungal microbiota of the external auditory canal were comprehensively analyzed by pyrosequencing on an FLX-454 platform. Of 17 samples tested, the fungal microbiota of 14 samples were composed of > 90% Malassezia species; either M. slooffiae or M. restricta was abundant in individual samples. The external auditory canal exhibits a lower fungal diversity than do other bodily sites.