ABSTRACT: Anthropogenic stresses on the naturally oligotrophic Gulf of Aqaba over the last 50 yr are suspected to have had a strong impact on biota, but the status of benthic fauna on the extensive soft-sediment seafloors is unknown. This study represents the first research on possible anthropogenic impacts on benthic marine fauna other than corals in the Gulf of Aqaba, a region of exceptional biodiversity. Comparing the species and functional-group composition of the living bivalve community to dead-shell assemblages from the modern seabed (top 5 cm) at 15 and 30 m water depth, both proximal and distal to historic point sources of nutrients, reveals that the ecological baseline has shifted. Live-dead discordance is strongest in the area of former sewage outfall and fish farm operations where seagrass is now functionally absent, but molluscan trophic structure has changed significantly even at distal sites where seagrass is still moderately abundant. Chemosymbiont-bearing lucinid bivalves specialized to sandy seagrass dominate death assemblages but are scarce to absent in living assemblages, which are dominated instead by facultative deposit-feeding bivalves which prefer muddy sand or muddy seagrass, consistent with organic enrichment. Seagrass habitat has thus changed qualitatively even where it persists, and sites of seagrass loss have not recovered despite cessation of major pollution ≥10 yr ago. Although shells of dead-only species require geological age-dating to definitively establish human drivers, the documentation of significant habitat change and trophic restructuring makes a powerful case for adoption of paleontological analysis by environmental managers and conservation biologists.