Isospora species are protozoan parasites that commonly infect the intestinal tracts of dogs and cats, leading to symptoms such as diarrhea and abdominal discomfort. The purpose of the study was to detect the parasites Isospora spp. in cats and dogs (both domestic and stray) of various ages and sexes in Basrah Governorate. Using microscopic examination with the flotation method, the infection rate with Isospora spp. in dogs was 9.5% (2/21), and in cats, it was 10% (11/109). Molecular analysis using PCR was performed on positive samples to confirm the infection with Isospora spp. and to identify the species based on the host. The study found that Isospora canis infects dogs, while Isospora rivolta and Isospora suis infect cats. This is the first recorded case of Isospora infection in cats in Basrah.