Identifying coastal flooding deposits within sedimentary records remains a challenge that requires the development of novel proxies. Here, we report the discovery and characterisation of marine organisms sedimentary ancient DNA in the 1755 Lisbon tsunami and younger paleostorm deposits from Martinhal, Portugal. We applied a metabarcoding approach and demonstrated that 102 eukaryotic molecular taxa including seaweed, molluscs and protists occur exclusively in modern marine sediments or marine coastal flooding (storm, tsunami) deposits from the past. We show that ancient DNA might be preserved in harsh and unstable conditions of the temporarily flooded lagoon in the warm and arid climate of Southern Europe. Moreover, diatom DNA is more frequently recorded compared to frustules in micropaleontological investigations of the same samples. Despite many advantages, the presented approach did not allow to differentiate between tsunami and storm deposits. Collectively, our findings highlight the potential of incorporating molecular biology techniques into the multi-proxy toolkit of coastal geologists and reveal the limitations of this emerging method.