Mapping and conservation assessment of wetland ecosystems is a necessary step in promoting effective management of wetland habitats by providing a uniform and comprehensive inventory of both common and rare types. The statewide distribution of wetland, deepwater, and upland habitats presented here represents the first effort to map wetlands in accordance with the national wetland classification system at medium-scale resolution for Alaska. We inferred wetland and deepwater type and distribution using land cover and hydrographic data as proxy indicators. Additionally, rare wetland ecosystems are described, mapped, and conservation status ranked. The final map included 2,211 unique land cover classes and approximately 4,600 wetland and deepwater equivalents. Overall map accuracy was 69% with a Kappa statistic of 0.64, indicating fair accuracy. When assessed at the wetland system level, accuracy ranged from 50 to 93%, with the Marine system mapped with the lowest accuracy and with the Riverine system mapped with the highest accuracy. The statewide wetland, land cover and rare ecosystem maps are served through an interactive data portal administered by Alaska Center for Conservation Science at University of Alaska Anchorage.