Phragmites marshes, which are found in every continent except in Antarctica, are being removed by resource managers in the US because it is considered an invasive species with little ecosystem service value. Here we present a comprehensive study on the ecosystem service value of an invasive Phragmites marsh vs a native Typha marsh for flood protection during tropical cyclones. Using a vegetation-resolving three-dimensional surge-wave model and observed vegetation and building data, we assessed the value of the Piermont Marsh in buffering Piermont Village, New York, USA from wave, flood, and structural damage during Superstorm Sandy in October 2012. Observed and simulated wind and water level data along the Hudson River were used as boundary conditions. Model results showed that the Marsh, with predominantly invasive Phragmites australis, dissipated more than half of the wave energy, but negligible flood, at the Village during Sandy. River-borne debris could not be transported across the Marsh to the Village. If Phragmites were replaced with the shorter, native cattail, Typha angustifolia, simulations of Sandy suggested that Piermont Marsh’s wave and debris buffering capacity would be preserved. However, had Sandy occurred in non-growth season when Typha is much shorter and sparser, the Marsh would be unable to buffer the wave and debris. Simulated residential structure damage during Sandy (>$10 M) agreed well with reported losses. If the Marsh were absent, the total loss would have increased by 26%. Since damage is dependent on the storm characteristics, we estimated the protective value of the Phragmites marsh for a 1% annual chance flood and wave event to be more than $2 M. This confirms the significant value of Piermont Marsh in protecting Piermont Village from flood and wave damage. To develop a balanced restoration plan, marsh managers should consider biodiversity as well as the significant ecosystem service value of Phragmites-dominated marsh for flood protection.