A new Coccidia species is reported from the natural population of Pied Flycatcher (Ficedula hypoleuca) in northern Germany. Sporulated oocysts were found in faeces from 6 of 8 sampled adults. The spherical oocysts of the new Isospora species have a brownish, smooth, bi-layered wall. Average size of sporulated oocysts was 19.4 x 19.3 microm (17.5-22.8 microm x 17.5-22.8 microm ) with a shape index (length/width) of 1.0. The sporulated oocysts have no micropyle or residuum, but enclose several small polar granules that often cluster into 2-3 dumbbell-shaped formations. Sporocysts are slightly elongated, rounded at the end opposite the Stieda body, 15.3 microm x 9.2 microm in size (13.8-16.1 microm x 8.5-10.3 microm ), and have a shape index of 1.7 (1.6-1.8). The Stieda body has a prominent knob-like cap, whereas the substieda body is absent. Sporocysts contain a small compact sporocyst residuum and 4 sporozoites. COI haplotypes identical to those isolated from faecal oocysts were PCR amplified from the blood of 13-day-old nestlings, suggesting that the newly described species has extra-intestinal stages in blood. This represents the first description of a new avian Isospora species supported by molecular sequence data from the same oocysts that are described morphologically.