In a detailed investigation of the sedimentology, mineralogy and trace element geochemistry of the stratigraphic interval spanning the Paleocene/Eocene (P/E) boundary in the Gabal el-Qreiya section, the author attempts to reconstruct environmental changes across the boundary especially for the interval representing the Paleocene-Eocene Thermal Maximum (PETM). The PETM interval consists of three distinct thin units of phosphatic shales followed by a calcareous phase. The basal unit is a laminated clay layer, whose base represents the base of the Eocene. It is enriched in silica and aluminium and is slightly phosphatic (bone-bearing). The middle unit is CaCO3-rich and bone-bearing, with a higher proportion of phosphatic components than the basal clay layer. The upper unit is coprolite-rich. These sediments contain different abundances of barite, Mn-oxide particles and grains of detrital origin. The PETM interval at Gabal el-Qreiya is characterized by high anomalies in most chalcophiles and REEs especially in the basal clay layer and the bone-bearing bed. It is concluded that these trace elements are incorporated into the phosphatic components (fish debris and coprolites) and organic matter. The three phosphatic shale units reflect euxinic marine environments and deposition in anoxic H2S-containing bottom waters rich in organic matter. The sedimentological, mineralogical and geochemical data show that the PETM interval represents deposition in a relatively deep water environment. However, it reflects slight fluctuations of sea level, a humid climate, high rain fall and oxidation conditions during weathering.