Parasitological examination of European otter originating from Extremadura, Spain revealed the presence of a new isosporan species. Oöcysts of Isospora lutrae n. sp. are spherical to subspherical, 31.2 (27.5–32) × 29.6 (28–31) μm and have a smooth wall c. 1 μm thick. Sporocysts are ellipsoidal, 18.2 (17–19) × 14.4 (14–16) μm and lack Stieda and substieda bodies. A spherical sporocyst residuum is present, consisting of granules scattered among the sporozoites. Sporozoites are spindle-shaped, 12.4 × 2.5 μm and have anterior and posterior refractile bodies. Based on its unique morphologic structure and host, I. lutrae is considered to be new.