Small ruminant infections by the Cysticercus tenuicollis result in financial losses because of the condemnation of infected organs, which can happen in unsanitary conditions and is regarded as an ecotoxicological risk factor. Therefore, a cross-sectional study was conducted to investigate the infection rate of Cysticercus tenuicollis, risk factors, and morphological, histological, biochemical, and molecular characterization of the genetic sequence of cysts collected from the affected organs of 139 sheep and 261 goats in the Allam-ELrom abattoir, Matrouh Governorate, Egypt. The overall infection rate was 19.25%, with a higher prevalence in goats, 23.40%, compared to sheep, 11.50%, indicating that species served as a significant risk factor for infection. However, no notable significant differences in infection rates were observed based on age or sex, with the main symptoms being pulmonary crackles by auscultation and visceral pain. The cysts were most frequently found in the omentum, 72.76%, followed by the liver, 18.18%. There were significant differences in biochemical parameters, such as liver enzymes and lipid profiles of the cyst fluid, among different organs. Molecular identification through PCR and sequence investigation of the cox1 gene in goats and 12S rRNA in sheep confirmed the cysts as C. tenuicollis. The retrieved sequences (OL470129 for sheep and OL470130 for goats) were nearly identical to those reported from other countries, highlighting the genetic similarity of this parasite across regions.