This study documents palynomorph assemblages from the Oligocene through the Early Miocene, across the significant Warm-house to Cool-house transition, using a subsurface section from the AG-5 well, north Western Desert of Egypt. Although the Paleogene and Neogene strata occupied a large area of the land, little about vegetation and ecosystem processes that shaped the climate and biodiversity during this time window is known. Here, based on a comprehensive palynological analysis of the Oligocene to Early Miocene Dabaa and Moghra formations encountered in the AG-5 well, we show that the studied area was characterized by a humid tropical to subtropical climate during the Oligocene-Miocene time interval. The obtained results provide clear evidence of the poorly known Paleogene-Neogene ecosystem in North Africa. In terms of palynostratigraphical framework, three palynozones covering the late Oligocene-Early Miocene interval are recognized. Moreover, the recovered palynomorphs inferred a deposition of the Dabaa Formation under a normal marine, inner shelf to littoral environment. However, for the basal part of the Moghra Formation, a deposition in an offshore marine environment, outer shelf (high sea level, 100–200 m depth) is assumed, whereas a deposition in shallow coastal lagoons, estuary, or delta environment (low sea level) is presumed for its uppermost part.