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There are only a few reports about the occurrence of coccidia in peafowl and no reports about the occurrence of Eimeria spp. in peafowl kept in Europe. Here, we describe the occurrence of Eimeria pavonina in diseased peafowl from Germany. In January 2011, one young peacock kept in an aviary showed a marked depression. No parasites were detected in samples from the diseased bird, but in samples of birds from the same and other aviaries, coccidian counts were between 400/g and 66,000/g. All peacocks were treated with toltrazuril. After treatment, the clinical condition of the diseased bird improved but, two weeks afterwards, other birds in the aviary were still shedding coccidia in their feces. Based on morphology, the coccidia were identified as E. pavonina. Parts of the 18s rRNA gene and the cytochrome oxidase subunit 1 (cox-1) gene were sequenced. A phylogenetic tree based on the 18s rRNA sequence placed the Eimeria sp. from peafowl closest to Eimeria spp. found in pheasants and partridges as well as to Eimeria meleagrimitis. A phylogenetic tree based on the sequence of cox-1 in contrast suggested a closer relationship to Eimeria necatrix and Eimeria tenella.