The eastern Mediterranean marine ecosystem is undergoing massive modification due to biological invasions, overfishing, habitat deterioration, and climate warming. Our ability to quantify these changes is severely hindered by the lack of an appropriate baseline; most ecological datasets date back a few decades only and show already strong signatures of impact. Surficial death assemblages (DAs) offer an alternative data source that provides baseline information on community structure and composition. In this study, we reconstruct the marine fish fauna of the southern shallow Israeli shelf before the opening of the Suez Canal based on fish otoliths. We quantify the age of the otolith DAs by radiocarbon dating, and describe its taxonomic composition, geographic affinity, and trophic structure. Additionally, we test by radiocarbon dating the hypothesis that Bregmaceros, a presumed Lessepsian invader with continuous presence in the Mediterranean throughout the late Cenozoic, is a relict species. The otolith DA dates back to the mid-Holocene because 75% of the dated otoliths of the native species are older than the opening of the Suez Canal in 1869, suggesting that the DA is a proper baseline for quantifying modern impacts. Consistently, 97% of the otoliths and 88% of the species we collected belong to native Mediterranean species. The native anchovy Engraulis encrasicolus dominates the DAs, although gobiids are the most diverse group (14 species, 28%). The DAs show similar trophic structure to present-day pristine Mediterranean coastal fish assemblages. Two non-indigenous species are recorded here for the first time in the Mediterranean Sea, Amblygobius albimaculatus and Callogobius sp., highlighting the importance of DAs for detecting non-indigenous species. Finally, Bregmaceros otoliths are modern, not supporting the previous hypothesis that the taxon is a Pleistocene relict.