Quail meat has gained a reputation as an outstanding source of protein and other essential nutrients, giving it numerous advantages over other poultry species. However, quail production has some limitations. One of them is vulnerability to parasitic infections that produce severe economic losses. Consequently, this study aimed to determine the prevalence and molecular characterization of Anonchotaenia species infecting quails in Elbehera Governorate, Egypt. A total of 239 quails were examined for gastrointestinal parasites. The total prevalence of Anonchotaenia infection was 0.83%. The prevalence was 1.11% in the Edko district, but no infection was recorded in Rashid. The prevalence of infection in migrant quails was 2.21%, while no infection was recorded in domesticated quails. The prevalence was higher in males than in females. The 18S rRNA sequence of Egypt’s Anonchotaenia species has 99% identity with Anonchotaenia brasiliensis. The phylogenetic tree of the 18S rRNA showed that sequence of Anonchotaenia sp. from Egypt is in the same clade as Anonchotaenia macrocephala from Brazil and Chile. Molecular characterization using 18S rRNA gene sequencing is valuable for parasitic helminth genetic identification in quails. The results presented a novel member of the genus Anonchotaenia in quails from Elbehera governorate, Egypt for the first time.