Objective To present the molecular characterization of Cysticercus tenuicollis (C. tenuicollis) of Taenia hydatigena (T. hydatigena) from livestock isolates in Egypt, and to introduce a detailed image of C. tenuicollis infection in ruminant animals in Upper Egypt. Methods The prevalence rates of C. tenuicollis infections among the slaughtered animals from different organs were determined using the amplification of sequencing of the MT-CO1 gene. Results In the present study the infection rates of C. tenuicollis were found to be 16% and 19% in sheep and goat samples respectively. Firstly we report one larval stage of T. hydatigena detected in the camel liver in Egypt. C. tenuicollis infection manifested a higher prevalence in females than in males. Those above two years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goats. The molecular characterization using the MT-CO1 gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the C. tenuicollis parasite especially when the morphological character cannot be detected, because the metacestodes are frequently confused with infection by the hydatid cyst, especially when these occur in the visceral organs. In the present study, C. tenuicollis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 base pair). Conclusions Clearly molecular diagnosis for C. tenuicollis infection significantly helps to differentiate it from such other metacestodes as hydatidosis, which manifests a completely different pathogenicity and requires different control programs.