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A novel Eimeria sp. from a captive‐bred bilby (Macrotis lagotis Reid, 1837) has been identified in Western Australia. The bilby was bred at the Kanyana Wildlife Rehabilitation Centre, Perth, as part of the National Bilby Recovery Plan. Oocysts (n = 31) irregular blunt ellipsoidal, 17–18 × 11–12 (17.2 × 11.3); length/width (L/W) ratio 1.4–1.5 (1.5). Wall bi‐layered, 0.8–1.0 (0.9) thick, outer layer smooth, c.2/3 of total thickness. Micropyle barely discernible. Oocyst residuum is absent, but 2–3 small polar granules are present. Sporocysts (n = 31) ovoidal, 7–8 × 5–6 (7.8 × 5.7); L/W ratio 1.3–1.4 (1.4). Stieda, sub‐Stieda and para‐Stieda bodies absent or indiscernible; sporocyst residuum present, usually as an irregular body consisting of numerous granules that appear to be membrane‐bound or sometimes diffuse among sporozoites. Sporozoites vermiform with a robust refractile body. Further molecular characterization was conducted on the sporulated oocysts. At the 18S locus, it sat in a large clade of the phylogenetic tree with two isolates of Eimeria angustus from quendas (Isoodon obesulus Shaw, 1797) and the Choleoeimeria spp. It shared the highest identity with E. angustus (KU248093) at 98.84%; at the COI gene locus, it was unique and most closely related to Choleoeimeria taggarti, which is hosted by another species of marsupial, the yellow‐footed antechinus (Antechinus flavipes flavipes), with 90.58% genetic similarity. Based on morphological and molecular data, this isolate is a new species and named as Choleoeimeria yangi n. sp. [ABSTRACT FROM AUTHOR]