Coccidian protozoan species recorded from flycatchers are few, but they have been described with a certain frequency in recent years. In this context, the present study describes a new Isospora sp. from sepia-capped flycatchers Leptopogon amaurocephalus Tschudi, 1846 captured in the Itatiaia National Park and in a reforestation area which is about 60 km away from the park boundaries, in addition to providing a molecular identification via sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene. Isospora leptopogoni n. sp. has oöcysts that are subspheroidal to ovoidal, measuring on average 22.0 × 19.7 μm, with a smooth, bi-layered wall, c.1.7 μm thick. The micropyle is delicate or inconspicuous. Oöcyst residuum is absent, but one to three polar granules are present. Sporocysts are lemon-shaped, measuring on average 14.7 × 9.3 μm, with a knob-like Stieda body and a rectangular to rounded sub-Stieda body. Sporocyst residuum is present, consisting of compactly bounded granules. Sporozoites are vermiform, with refractile bodies and nucleus. Isospora leptopogoni is different from other Isospora spp. mainly due to its lemon-shaped sporocysts, the presence of micropyle and details of Stieda and sub-Stieda bodies. Phylogenetic analysis placed I. leptopogoni close to other Isospora spp. recorded from phylogenetically related hosts and from the same biogeographic region. Finally, the recurrent finding of this coccidian species in the same L. amaurocephalus specimen in a specific locality in the Itatiaia National Park suggests that the dispersion of I. leptopogoni needs continuous transmissions between susceptible passerines as the area of movement of each L. amaurocephalus specimen appears to be quite small.