Integrated high resolution calcareous planktonic nannofossil and foraminiferal biostratigraphic studies are carried out on the Paleocene/Eocene (P/E) boundary at Gebel El Aguz and Gaga on the eastern plateau of the Kharga-Baris oases, Western Desert, Egypt. The five beds of the Dababiya Quarry Member of the Esna Formation are represented partially on the study sections. At G. El Aguz beds nos. 1–4 are missing, whereas at Gaga bed no.1 is absent which indicates the occurrence of a hiatus with different magnitude. This hiatus is documented by the occurrence of irregular surface with pebbles at G. El Aguz and the occurrence of glauconitic layers at Gaga section. Biostratigraphically, the P/E boundary is defined at the NP9a/NP9b nannofossil zonal boundary which is equivalent to the Morozovella velascoensis (P5)/Acarinina sibaiyaensis (E1) at Gaga section and A. soldadoensis/Globanomalina pseudomenardii (P4c)/A.sibaiyaensis (E1) planktonic foraminiferal zonal boundaries at G. El Aguz with interzonal hiatus. This indicates that the sedimentary basin during the P-E interval at the study area was unstable and affected by a tectonic event may be due to the echo of the Syrian Arc Orogeny.