At a routine health check of a female peregrine falcon, 23 trematodes preliminary identified as Prosthogonimus sp. were removed from the bursa of Fabricius. Based on morphological and molecular examination, a new species, Prosthogonimus falconis, was described. The pear-shaped flukes were 4.3–6.9 mm long, with greatest width posterior to testes. Tegumental spines measuring between 17 and 21 μm long covered the whole body. Length and width ratio of oral to ventral suckers were 1:1.3. Extracaecal, multifollicular vitelline glands commenced prior to acetabulum and terminated posterior to testes. Eggs in the distal uterus measured 21 × 12 μm. Molecular analysis of internal transcribed spacer 2, cytochrome c oxidase subunit 1 and NADH dehydrogenase subunit 1 gene regions revealed that the new species described here is phylogenetically closest to Prosthogonimus cuneatus and Prosthogonimus pellucidus clusters.