The adult worm Taenia hydatigena is a tapeworm with definitive hosts, such as canines. In contrast, the larval stage of T. hydatigena, known as the Cysticercus tenuicollis cyst, is found mainly in small and large ruminant animals and acts as an intermediate host. However, misdiagnosis and cross-reaction with other taeniasis species have prompted the use of molecular identification tactics to accurately diagnose both the metacestode (C. tenuicollis cysts) stage and the adult worm. This study addresses these concerns, which have not been previously studied at the molecular level in Egypt. C. tenuicollis cysts were collected from the general Matrouh governorate abattoir in Egypt, and adult worms were obtained from an experiment on native Egyptian dogs. The samples were molecularly identified using 12S and 18S rDNA sequences, and a phylogenetic tree was built to identify their relatives in GenBank. The study’s results showed that the 18S rDNA gene sequence of the adult worm was approximately 480 bp, similar to T. hydatigena with the GenBank accession number OL470118. The 12S rDNA sequencing of the cyst yielded an amplicon of approximately 450 bp that belongs to the T. hydatigena larval stage with the GenBank accession number OL470131. It is concluded that carnivorous animals, such as dogs, can pose a risk to small ruminant animals and have a negative impact on them. Therefore, it is recommended that periodic deworming should be performed for stray or farm dogs using different anthelmintic drugs.