Near infrared color aerial photography (-1:7200) of Yaquina Bay, Oregon, flown at minus tides during summer months of 1997 was used to produce digital stereo ortho-photographs covering tidally exposed eelgrass habitat. GIS analysis, coupled with GPS positioning of ground-truth data detected Zostera Japonica communities (non-indigenous eelgrass), which are physically separated by elevation in this and similar Pacific North-west coastal estuaries from Zostera marina (native eelgrass) communities. The non-indigenous Z, japonica typically occurs at or near mean high water while native Z, marina is restricted to -0.7 m above mean low water and below. Recognition of Z, japonica patches from adjacent bare sediment and emergent beach or marsh grasses was aided by combining specifically tailored detection algorithms and 'heads up' digitizing with digital bathymetry. Further progress in algorithm development should allow areal delineation, mapping and change analysis.