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Abstract Background Cystoisospora felis or Isospora felis is a ubiquitous apicomplexan protozoon parasite infecting domestic cats worldwide. Objectives of the study this study aims to identify the causative agent of diarrhea in cats by determining several elevating stressors caused by these coccidian protozoans with molecular characterization. So, from January 2023 to April 2023, a total of 370 domestic cats were hospitalized at various clinics in the Cairo and Giza Governorates. Fecal samples were taken from these animals and examined by concentration floatation techniques using a saturated salt solution. The positive samples were sporulated to identify the collected oocyst. Venous blood was taken from the infected cats to evaluate the associated oxidative stress marker (lipid peroxidation products (MDA). Results Out of 370 examined domestic cats, 27(7.29%) were positive for C. felis. The MDA levels increased with age, and females were higher than males. DNA was extracted from fecal samples for amplification of the ITS1 gene, followed by sequencing. The ITS1 gene was amplified and showed bands at 224 bp. The partial nucleotide sequence of the ITS1 gene was aligned with the reference sequences. In a conclusion C. felis increases the free radicals, which in turn means the animals have stress and need a schedule to treat these animals with new, safe protocol drugs that give no resistance and are highly efficient.