Abstract Capillaria Zeder, 1800, parasitizes the organs and tissues of several hosts, including the domestic duck Cairina moschata (Linnaeus). This article describes a new species of Capillaria in domestic ducks identified based on morphological studies and molecular analyses of the ribosomal RNA gene. Thirty-eight specimens of C. moschata from the municipality of Soure, Marajó Island, Pará, Brazil. The organs of the birds' digestive tract were analyzed under a stereomicroscope to confirm the parasitic infection, after which the collected nematodes were identified by light microscopy, scanning electron microscopy, and molecular analysis. Capillariids parasitized the intestine and cecum of the examined birds. These parasites had three bacillary bands and a pair of elongated precloacal papillae on the tail. Phylogenetic analysis indicated that the new species formed a sister clade with Capillaria spinulosa (Linstow, 1890), as described in Indonesia and Japan. Based on morphological distinctions and molecular data, Capillaria cairina n. sp. can be considered a new parasite species of C. moschata in the Brazilian Amazon.