Blue carbon ecosystems, particularly seagrass meadows, provide a myriad of critical ecosystem services through their role in supporting biodiversity, protecting shorelines, and sequestering and storing carbon. Despite their increased recognition for advancing global marine conservation efforts, our knowledge of the location and spatial extent of seagrass ecosystems globally remains relatively poor, due to the logistical and operational challenges of accurately mapping seafloor habitat using remote sensing techniques. Here we develop and validate an aerial LiDAR approach for mapping tropical seagrass blue carbon habitat in The Bahamas, by integrating full waveform bathymetric LiDAR with multi-spectral imaging. The results demonstrate accuracies between 92 and 98% for predicting seagrass types, over an extensive (e.g., >1000 km(2)) study area whilst utilizing robust ground-truthing techniques. These findings demonstrate the value of the aerial LiDAR approach used here for ongoing bathymetric surveys of seagrass habitat in The Bahamas and throughout similar ecosystems in the wider Caribbean, which should provide key insights for coastal management and conservation efforts.