Biological and physical factors govern the distribution of fossils, but it is not always clear which is more important. The preservation of late Eocene vertebrates at the UNESCO World Heritage site of Wadi Al-Hitan, Western Desert of Egypt, is controlled primarily by the physical processes responsible for sequence stratigraphic architecture on a siliciclastic shelf. Three types of stratigraphic surface, each characterized by a taxonomically and taphonomically distinct fossil assemblage, yield most of the known vertebrate fossils. Complete, partially articulated whale skeletons, primarily Basilosaurus isis, are abundant in offshore marine flooding surfaces (MFS) in the late transgressive systems tract (TST) of the first Priabonian sequence (TA4.1), where low net sedimentation rates and environmental averaging in offshore environments promoted the accumulation of carcasses on traceable stratigraphic surfaces. Complete, well-articulated whales, primarily Dorudon atrox, are more widely scattered on minor erosion surfaces in rapidly accumulating shoreface sediments of the overlying falling stage systems tract. Fragmented and abraded vertebrate remains are abundant and diverse in a discontinuous conglomerate that marks the first sequence boundary above the base of the Priabonian (Pr-2), which has not been previously recognized in Egypt, but which formed incised valleys with at least 45 m of total relief. Fossils in this variably thick lag conglomerate include skeletal elements reworked by rivers from underlying marine deposits and bones of terrestrial animals living in the fluvial environment. Marginal marine vertebrates, primarily dugongs, occur on shelly marine ravinement surfaces above Pr-2, in the early TST of the second Priabonian sequence. Most vertebrate remains in Wadi Al-Hitan occur in condensed stratigraphic intervals and taxonomic composition changes with sequence position, both important considerations in interpretation of paleobiological patterns.