As a result of the previous studies over the past few years, a number of intriguing characteristics regarding the relationships between various mammalian populations across the Isthmus of Suez have been emerging. The mammalian populations in Sinai and Africa differ by this isthmus. All animals inhabiting the Egyptian Western Desert and Sinai Peninsula cannot cross the Nile Delta and Valley, as well as the Isthmus of Suez, which together represent significant ecological barriers. Fourteen skulls of the fennec fox "Vulpes zerda" that have been stored in Al-Azhar University Zoological Collection (AUZC) at Al-Azhar University (Cairo, Egypt) were used in the current study. These skulls were collected between 1983 and 2007 from the Egyptian Western Desert and Sinai Peninsula. The absolute cranial and dental measurements used here showed significant differences (P<0.05) between the two studied populations. The cranial and dental measurement ratios also showed significant differences (P<0.05) between the two studied populations. Thirteen differences between the fennec fox skulls from the two studied populations were detected. These differences may be enough to make the two populations separate from each other taxonomically, perhaps at the subspecies level. Principal component analysis of the cranial and dental measurements used in the current study confirmed the differences between the two studied V. zerda populations. More future studies should take place to confirm or deny the separation of these populations at the subspecies level.