Black-footed ferrets (BFF; Mustela nigripes) are the only ferret species native to North America and have been listed as endangered since 1967. Starting in 1986, a multi-institutional effort has been breeding this species in captivity with successful reintroductions back into the wild. Enteric coccidiosis is recognized as a frequent cause of juvenile morbidity and mortality in captive breeding programs, and can result in substantial population losses. Despite this, little is known about the etiology of coccidiosis in BFF. Coccidia-positive fecal samples (n=12) and formalin-fixed paraffin-embedded intestinal tissues (n=11) were obtained from BFF in the Toronto Zoo (Ontario, Canada) and Louisville Zoo (Kentucky, USA) Species Survival Plan (SSP) populations. Oocyst morphometrics and sequence genotyping at three loci (nuclear 18S rDNA, mitochondrial cytochrome c oxidase subunit I and mitochondrial cytochrome c oxidase subunit III) were conducted to characterize the coccidium or coccidia responsible for disease outbreaks in these ferrets in different age classes and years. Results suggest that a single Eimeria species, E. ictidea, was the cause of enteric coccidiosis in both SSP populations in both juvenile and adult age classes in all years evaluated. Wider research is indicated to determine whether these findings are representative of the broader captive and wild BFF populations.