Skulls are a critical part of the crocodile through which we can distinguish between the different genera and species. Most of the crocodiles which previously studied from the Eocene-Oligocene to the Miocene times in Egypt were concerned with the identification of the genus and sometimes on the species without a detailed focusing on the evolution, comparing between them and trying to determine the ancestor or the closest species of them to the living crocodile in Egypt. The only known living species of Crocodylus in Egypt is Crocodylus niloticus which inhabits Lake Nasser in Aswan, southern of Egypt. From the Cenozoic era, broad snouted crocodiles diversity had been reported in Egypt. About 35 million years ago, through the Eocene epoch, the crocodilian fossils from Fayum provided evidence of the diversity of crocodile species including Crocodylus articeps and Crocodylus megarhinus. In addition to that, throughout the Early Miocene epoch, from about 18 million years ago, in Wadi Moghra Egypt crocodilian fossils demonstrate another diversity, extended to the first appearance of Rimasuchus lloydi which placed inside the Osteolaeminae later. By various measurements and carefully morphological examination of the different species recorded from Egypt, it was found that there are high levels of variation in morphology of the skulls including their dimensions, and the sutures shapes especially between premaxilla and maxilla ventrally and also between maxilla and palatine, as well as the extension of the maxillary ramus of the ectopterygoid. Using cluster analysis, it is proven that Eocene Crocodylus is the ancestor to all known broad snouted species recorded from Egypt since the Eocene time. The closest species to the Eocene specimen is the living Crocodylus niloticus. That in fact make that most of the broad snouted crocodiles in Egypt are endemic.