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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 …