We found the ear mite parasite (Otodectes cynotis; Acari: Psoroptidae) in two distant insular endangered fox populations in Chile. We identified O. cynotis in both the Darwin's fox (Pseudalopex fulvipes) from Chiloé and the Fuegian culpeo (Pseudalopex culpaeus lycoides) in Tierra del Fuego. These populations are approximately 2,000 km apart. Infestation rates were high for both endemic foxes: 76% (19/25) of Darwin's foxes were affected, and 73% (11/15) of Fuegian culpeos had ear mites. Two Darwin's foxes had abundant ear discharge, and one of these also exhibited secondary infections of Morganella morganii and Geotrichum sp. fungi. Mites were characterized molecularly as Otodectes spp. for the Fuegian culpeo samples. Genetic analyses of two mites found the O. cynotis genotype I, as well as what appeared to be a new allele sequence for O. cynotis. These results confirmed the hypothesis of a worldwide distribution species of ear mite. Introduced chilla foxes (Pseudalopex griseus; n=11) on Tierra del Fuego Island and domestic dogs (Canis lupus familiaris; n=379) from both islands were also sampled, but they showed no signs of infection. Our findings provided insight into the genetic diversity, the origins, and the possible impact of this globally distributed mite on endemic free-ranging populations of foxes.