We aimed to identify faeces belonging to either Darwin’s fox (Lycalopex fulvipes) or kodkod (Leopardus guigna) by using molecular genetic techniques, and to describe and compare the gastrointestinal parasites harbored by both carnivores in Chiloé Island. We found that 60% (25/42) and 88% (28/32) of faeces of Darwin’s fox and kodkod had parasite eggs. This study provided the first record of Aspiculuris sp. and trematodes in Darwin’s fox and Aspiculuris sp., Trichuris sp., Capillaria sp., Isospora sp. and trematodes in kodkod, which may correspond to either prey- or host-originated parasites.