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Sea-level changes, palaeobathymetry, palaeo-productivity and depositional sequences (sequence stratigraphy) are evaluated using benthic foraminifers from two subsurface boreholes in the North Western Desert (Egypt) belonging to the Eocene Apollonia Formation. Five planktic foraminiferal biozones (E4-E5, E8-E10) have been identified. The absence of E6-E7 and upper Eocene zones are attributed to long-time unconformities (regional tectonics) during the Cretaceous/Palaeogene (K/Pg) and Eocene/Oligocene (E/O) boundaries with estimated time gaps of 16 and 13.9 Ma, respectively. Six benthic foraminiferal assemblages, spanning middle to outer neritic depths, are noted. They are represented by Bolivinoides decoratus, Eponides mariei, Bulimina quadrata, Anomalinoides zitteli, Uvigerina eocaena and Uvigerina pygmoides. Three depositional sequences based upon four sequence boundaries are also identified. Each depositional sequence can be classified into transgressive and highstand system tracts inferred from benthic foraminiferal palaeobathymetry, which are separated by maximum flooding surfaces (MFS), characterised by maximum abundance of buliminids and uvigerinids, and peak values of total foraminiferal numbers, planktic (P)% and diversity. Comparisons of our recorded sequences and their boundaries inside and outside Egypt reflect that the studied succession is affected by both tectonic activity that caused long time gaps and eustatic processes.