Zoonotic protozoan parasites in dogs represent a significant public health concern because of their ability to infect humans. This study aimed to detect and determine the prevalence of zoonotic protozoan infections, including Balantidium coli, Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., Sarcocystis spp. and Cystoisospora spp. in stray and owned dogs with diarrhea in Trabzon Province, Türkiye. Fecal samples were obtained from 450 dogs of various ages, sexes, and breeds. Samples were preserved in 70% alcohol for molecular analysis and incubated in 2.5% potassium dichromate for microscopic examination. Parasite DNA was analyzed using polymerase chain reaction (PCR) and identified by restriction fragment length polymorphism (RFLP). Microscopic examination identified the Cystoisospora ohioensis group, Cystoisospora canis, and Sarcocystis spp. in 56 samples (12.44%). Specifically, Cystoisospora spp. and Sarcocystis spp. were detected in 36 (8.00%) and 20 (4.44%) of the samples, respectively. A mixed infection involving C. canis and the C. ohioensis group was observed in one sample. Molecular analyses detected Cystoisospora spp. DNA in 36 samples (8.00%) and Sarcocystis spp. DNA in 20 samples (4.44%). RFLP analysis confirmed that all detected Cystoisospora spp. DNA belonged to C. ohioensis, while Sarcocystis spp. could not be differentiated at the species level. This study reports the first microscopic detection of Sarcocystis spp. and C. ohioensis in dogs in Trabzon Province and constitutes the first molecular identification of C. ohioensis in Türkiye.