Eelgrass (Zostera marina) can provide vital ecological functions in stabilizing sediments, influencing current dynamics, and contributing significant amounts of biomass to numerous food webs in coastal ecosystems. Mapping eelgrass beds is important for coastal water and nearshore estuarine monitoring, management, and planning. This study demonstrated the possible use of high spatial (approximately 5 m) and temporal (maximum low tide) resolution airborne multispectral scanner on mapping eelgrass beds in Northern Puget Sound, Washington. A combination of supervised and unsupervised classification approaches were performed on the multispectral scanner imagery. A normalized difference vegetation index (NDVI) derived from the red and near-infrared bands and ancillary spatial information, were used to extract and mask eelgrass beds and other submerged aquatic vegetation (SAV) in the study area. We evaluated the resulting thematic map (geocoded, classified image) against a conventional aerial photograph interpretation using 260 point locations randomly stratified over five defined classes from the thematic map. We achieved an overall accuracy of 92 percent with 0.92 Kappa Coefficient in the study area. This study demonstrates that the airborne multispectral scanner can be useful for mapping eelgrass beds in a local or regional scale, especially in regions for which optical remote sensing from space is constrained by climatic and tidal conditions.