Due to increasing development Southeast Asia's coastlines are undergoing massive changes, but the associated impacts on marine habitats are poorly known. Singapore, a densely populated island city-state, is a quintessential example of coastal modification that has resulted in the (hitherto undocumented) loss of seagrass. We reconstructed the historic extent and diversity of local seagrass meadows through herbarium records and backwards extrapolation from contemporary seagrass locations. We also determined the current status of seagrass meadows using long-term monitoring data and identified the main threats to their presence in Singapore. Results show that, even though ~45% of seagrass has been lost during the last five decades, species diversity remains stable. The main cause of seagrass loss was, and continues to be, land reclamation. We conclude that strict controls on terrestrial runoff and pollution have made it possible for seagrass to persist adjacent to this highly urbanised city-state. © 2014 Elsevier Ltd.