The European bison, Bison bonasus is the largest terrestrial mammal in Europe; it is also on the red list, being recognized as vulnerable to extinction by the International Union for Conservation of Nature. The species suffers from low genetic variability, rendering it vulnerable to various environmental and biological threats.This study presents the first molecular confirmation of Eimeria bovis infection in European bison, and details a 1708 bp nucleotide sequence of the 18S rRNA gene in European bison-derived E. bovis (GenBank: MK691697). It also describes two multiplex PCR assays based on 18S rRNA gene for identifying Eimeria bovis oocysts and developmental stages in European bison and cattle. These yielded DNA banding patterns common for those of Eimeria spp. (250 bp for the first assay and 305 bp for the second assay) and species-specific E. bovis DNA in positive samples (344 bp and 586 bp, respectively). Both multiplex PCRs yielded bands characteristic of Eimeria spp. and E. bovis in samples containing DNA of oocysts from both bison and cattle. Moreover, convergent results were obtained for the DNA of the wall of colon in both assays, indicating the presence of developmental stages of Eimeria spp. other than E. bovis. Despite displaying the same sporulation time (four days), and similar general morphological features, the E. bovis oocysts derived from European bison were significantly narrower than those obtained from cattle (t = −6.19, p < 0.001), with a significantly higher shape index (length/width ratio) (t = 3.94, p < 0.001).The result provides further evidence for infection of European bison with a highly-pathogenic bovine protozoan, E. bovis.