The black-footed ferret (Mustela nigripes) is a native North American ferret species that has been endangered since 1967. Among the threats faced by M. nigripes is the eukaryotic parasite, Coccidia, which causes gastrointestinal diseases and contributes to a substantial population loss. In this study, fecal samples from two black-footed ferrets showing clinical signs of coccidiosis were examined microscopically for two consecutive days, and Coccidia oocysts were detected only in the samples collected on the second day. Metagenomic sequencing and Sourmash analysis were used to characterize the fecal microbiomes. The detected Coccidia species belong to the genus Cystoisospora. On day one, microbiomes were dominated by Escherichia coli, comprising 60-80% of the total relative abundance. Although no significant changes in alpha and beta diversity were observed between Coccidia-negative and Coccidia-positive fecal samples, distinct compositional shifts were evident. Specifically, the relative abundances of Bacteroides, Enterococcus, Fusobacterium, and Peptostreptococcus increased following the onset of Coccidia shedding. Peptostreptococcus russellii was significantly enriched in Coccidia-positive samples, whereas several commensal and potentially beneficial taxa, including Hafnia alvei and Cutibacterium acnes were significantly depleted. These changes suggest a transition toward gut dysbiosis and increased susceptibility to secondary bacterial infections as Coccidia infection progresses.