Cryptosporidium spp. are important enteric protozoa capable of infecting a wide range of vertebrate hosts, including cats. Although feline cryptosporidiosis is often subclinical, certain species such as Cryptosporidium felis possess zoonotic potential. Data on the prevalence and molecular characteristics of Cryptosporidium infections in cats in Türkiye remain limited. This study aimed to determine the prevalence, species distribution, and zoonotic relevance of Cryptosporidium spp. in cats from the Iğdır region. Fecal samples collected from 100 cats were examined microscopically using the Kinyoun acid-fast staining method and molecularly by nested PCR targeting the 18S rRNA gene. PCR-positive samples were sequenced using the Sanger method, and phylogenetic analyses were performed with MEGA 12 software. Microscopy detected oocysts in 1% (1/100) of samples, while nested PCR identified 3% (3/100) positivity. Higher prevalence was observed in females and in cats younger than one year; however, these differences were not statistically significant (P>0.05). All three sequenced isolates were identified as C. felis, showing 99.75% identity to reference sequences in GenBank. Phylogenetic analysis confirmed that all isolates clustered within the C. felis lineage. The presence of C. felis in cats in the Iğdır region highlights their potential role as reservoirs of zoonotic Cryptosporidium species. These findings underscore the importance of continued surveillance and molecular characterization of feline cryptosporidiosis in Türkiye, particularly due to the close human–cat interaction in domestic environments.