Histology of newly discovered ganoid scales from the lower Bahariya Formation, in the Bahariya Oasis of western Egypt, confirms the presence of polypterid osteichthyans in this early Cenomanian locality. These fossils, occurring in the ∼97 million-year-old lower Bahariya sequences, are among the earliest known polypterids. The Bahariya scales exhibit four tissues: ganoin, dentine, isopedine (elasmodin), and a basal plate of cellular bone, confirming their inclusion within the Polypteriformes. They have a discontinuous ganoin layer, present only as highly variable ridges and bosses. Dentine along the edges of the ganoin ridges appears to have undergone active remodeling, suggesting that the ganoin ridges represent the remnants of a continuous ganoin cover. Modern polypterids inhabit exclusively freshwater environments. Polypterids are not rare in the lower Bahariya Formation. Their presence in these coastal sediments suggests that freshwater habitats lay close to the site of deposition of this sequence during the early Cenomanian.