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 Isopora species have a brownish, smooth, bi-layered wall. Average size of sporulated oocysts was 19.4 x 19.3 mu m (17.5-22.8 mu m x 17.5-22.8 mu m) 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. Sporocytes are slightly elongated, rounded at the end opposite the Stieda body, 15.3 mu m x 9.2 mu m in size (13.8-16.1 mu m x 8.5-10.3 mu m), and have a shape index of 1.7 (1.6-1.8). The Stieda body has a prominent knob-like chip, 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 front the same oocysts that are described morphologically.