Biostratigraphy and paleoenvironment of seventy surface samples were studied based on calcareous nannofossils along the Upper Maastrichtian – Eocene sequence at Gebel Duwi and Gebel Ghanima sections, Egypt. This succession includes three rock units, arranged from base to top as follow: Dakhla, Tarawan and Esna formations. Seven calcareous nannofossil biozones have been recorded, arranged as follow: CC 25c, CC 26, NP 2/3, NP 4, NP 5, NP 6 and NP 9b, discussed and compared with their counterpart in and outside Egypt. Four present stage boundaries have been discussed; the Cretaceous/Paleogene boundary, it seems to be incomplete in the Gebel Duwi section due to the absence of the biozone NP 1. The Danian/Selandian boundary, it can be determined in the Gebel Ghanima section based on the FO of Fasciclithus tympaniformis. The Selandian/Thanetian boundary, it was difficult to trace in the Gebel Ghanima section, where the topmost part of Zone NP 6 was missed. The Paleocene/Eocene boundary, it cannot be accurately determined in the Gebel Ghanima section, owing to the presence of a small hiatus represented by the absence of the Subzone NP 9a. There is predominance in assemblages’ taxa and were relatively warm-water temperature during the Late Danian in the Gebel Duwi section and highly warm-water temperature around the Paleocene-Eocene boundary in the Gebel Ghanima section. There are two ecozones have been recognized in our study. In the Gebel Duwi, the sediments of ecozone (A) are deposited in cool-water, and transitional states between eutrophic and oligotrophic environments, while that of ecozone (B) are deposited in warm-water and also transitional states between eutrophic and oligotrophic environments. The sediments of ecozone (B) in the Gebel Ghanima are deposited in warm-water and mainly oligotrophic environments.