This work depends on the study of the lower part of the Esna Formation which encompasses the Paleocene–Eocene (P-E) transition in Egypt as well as at Naqb Assiut section, Kharga Oasis, Western Desert. The Paleocene/Eocene (P/E) boundary is represented by El Dababiya Quarry Member which consists of five distinctive beds (nos. 1–5) at the GSSP. On the other hand, at Naqb Assiut section this boundary is only represented by the upper two beds (nos. 4&5), whereas, the lower three beds (nos. 1–3) are missing due to a hiatus. This hiatus is marked by the occurrence of an irregular surface contains pebbles and phosphatic materials. This hiatus may be related to the echo of Sryian Arc Orogeny at the P/E time. Biostratigraphically; four planktonic foraminiferal zones are defined from base to top as: Acarinina soldadoensis/Globanomalina pseudomenardii and Morozovella velascoensis (late Paleocene), Acarinina sibaiyaensis and Pseudohastigerina wilcoxensis/Morozovella velascoensis (early Eocene). The Acarinina sibaiyaensis Zone which represents the P//E/boundary is characterized by the occurrence of intrazonal hiatus at it's lower part. The benthonic foraminiferal taxa contain abundant representatives of Midway-type fauna (∼91% of the whole assemblages), beside few Velasco-type faunal ones (∼9%), indicating an outer neritic (150–200 m) water depth of deposition during the P–E transition. Quantitative analysis and composition of benthonic foraminiferal assemblages are indicative for various environmental changes around the P/E boundary. They reflected a high diversity, increase of epifaunal taxa, and low-intermediate productivity conditions, which indicates a well-ventilated bottom water and oligo - to mesotrophic conditions during the late Paleocene age. Rapid extinction of about 18% of the entire benthonic foraminiferal species started at the P/E boundary, where the last occurrence of Angulogavelinella avnimelechi is pronounced at the base of this boundary. There is a decline in the preceding faunal characteristics of the late Paleocene and signified an increase in the abundance of agglutinated and buliminid species. These characters are revealed some environmental stressful conditions of low oxygen and increased productivity. During the early Eocene, the environmental conditions are improved leading to the recovery of most benthonic and planktonic foraminifera.