The terrestrial management plan for Palmyra Atoll includes large-scale removal of coconut (Cocos nucifera) as part of native forest restoration and contaminant remediation that will leave soils and vegetation communities profoundly altered. To inform those efforts and provide baseline data for restoration monitoring, woody stem crowns and vegetation communities at Palmyra Atoll were mapped using existing datasets and manual photointerpretation of high-resolution aerial imagery collected using uncrewed aerial systems. Coconut palm, grand devil's claws (Pisonia grandis), and numerous other species were delineated as either individual crowns, crown portions, or species patches. The extent of land area at high tide was also delineated based on vegetation patterns, topographic indicators, and deposition lines of vegetation litter and flotsam. Finally, in a novel “bottom-up” approach to vegetation community mapping, crown maps were used to delineate U.S. National Vegetation Classification System vegetation communities and other management areas. Of the more than 44,000 mapped crowns, coconut was by far the most abundant species, comprising nearly half of the mapped stems. By establishing a quantitative baseline for current habitat conditions, this project facilitates the integration of contaminant remediation recovery activities with habitat restoration planning, implementation, and monitoring at Palmyra Atoll. Results illustrate the appropriateness of the mapping approach for plant species-level censuses and cover estimation over relatively small areas to aid in inventory and monitoring and to facilitate management planning. The relatively simple mapping methods used in this study are appropriate for resource managers with limited human and computational resources to support automated mapping.