Enteric coccidiosis is a major cause of death in both juvenile and adult black-footed ferrets (BFF, Mustela nigripes) in captive breeding programs that reduces the availability of animals for release to their former North American range. Coccidiosis is poorly understood in BFF but in vivo experimental infection in this endangered host is untenable. The goal of this research was to better characterize the etiologic agents and natural history of enteric coccidiosis in BFF and to evaluate the domestic ferret (DF, Mustela putorius furo) as a model for experimental infection. Morphometric and molecular characterization of coccidia from BFF and DF was undertaken. Only Eimeria ictidea was identified in juvenile and adult BFF from 1999-2016 at the Toronto Zoo and from BFF at the Louisville Zoo in 2016. Eimeria furonis and Isospora (=Cystoisospora) laidlawi were identified in DF fecal and necropsy samples from Canadian and European diagnostic laboratories during 2008-2017. Molecular characterization of these parasites included generation of complete mitochondrial genomes and nuclear 18S rDNA sequences for Eimeria ictidea and Eimeria furonis from BFF and DF, respectively. Partial sequences were obtained from the same genetic targets from I. (=C.) laidlawi from DF. DNA isolation from formalin fixed paraffin embedded tissues and PCR amplicon sequencing permitted identification of coccidia in BFF and DF tissues dating from 1999 to present. Retrospective and prospective analyses of medical and pathology records supplemented with parasitological evaluation of repeated fecal samples was performed to determine the natural history of coccidiosis in captive BFF. Clinical signs and histopathologic changes associated with infection in BFF were as described previously in the published literature. Average yearly coccidia associated mortality rates were 0.53% in adults and 1.95% in juveniles. Domestic ferrets were confirmed as experimental hosts of E. ictidea isolated from BFF. Seven of 10 juvenile DF inoculated with oocysts from a BFF developed patent infections and mild clinical disease was observed in six of these seven. Infection was confirmed via morphometric, molecular and histologic examination of samples from infected DF. While much is still unknown about enteric coccidiosis in BFF, domestic ferrets provide a promising model for further investigation of this disease.