Sarcocystosis considerably occurs in a wide host range including animals, reptiles, humans, and birds. This study was conducted to determine the prevalence of Sarcocystis spp. using abattoir inspection, genetic characterization, as well as histopathology in water buffaloes in two provinces, Elbehera and Kafrelsheikh, Egypt. Specimens were collected from esophagus, tongue, and masseters of 400 slaughtered buffaloes in Elbehera (n= 215) and Kafrelsheikh (n= 185). Samples were examined macroscopically and histopathologically. Furthermore, genetic characterization of Sarcocystis spp. was performed using the 18SrRNA gene-based PCR. The total prevalence was 71.0% (75.3% and 65.9% in Elbehera and Kafrelsheikh, respectively). Aged buffaloes had a higher prevalence than young ones. Females had a higher prevalence than males. The esophagus was the most infected organ. Molecular analysis revealed that the recovered species was S. fusiformis. This is the first genetic characterization of S. fusiformis in water buffaloes from Elbehera and Kafrelsheikh, Egypt. Higher prevalence proposed the potential role of cats in the transmission of S. fusiformis, which, in turn, requires strict hygienic measures to protect animals and humans from infection.