The Wisconsin Wetlands Inventory (WWI) was conducted by the State of Wisconsin, USA using a classification system and methods that are similar but not identical to those of the National Wetlands Inventory (NWI). Dissimilarities between the two inventories present problems for applications that cross state boundaries, such as inter-state comparisons or compilation of regional wetland statistics. The methods and classification systems of the two wetland inventories were compared, and GIS coverages were analyzed where the two inventories overlap near the cities of Superior and Baraboo. The NWI mapped both wetland and deepwater habitats and included Lacustrine and Riverine deepwater habitats that were intentionally not mapped by the WWI. Of the 178 km² Superior study area, 52% was mapped as upland by both, 22% was mapped as wetland by both, 10% was mapped as Palustrine wetland by NWI but not WWI, and 6% was mapped as wetland by WWI but not NWI. Of the 281 km² Baraboo study area, 91% was mapped as upland by both, 2% was mapped as wetland by both, 1% was mapped as Palustrine wetland by NWI but not WWI, and 1% was mapped as wetland by WWI but not NWI. Errors of omission were found for both inventories, but errors of commission (i.e., areas incorrectly mapped as wetland) were found only for the NWI maps in the Superior study area, which were prepared using 1:80,000 black and white panchromatic aerial photos. In theory and in practice, the two inventories were nearly equivalent with regard to Palustrine wetland class and subclass. The WWI “hydrologic modifier” has fewer categories than the NWI “water regime,” but a preliminary conversion table was developed to recode the WWI digital maps to their equivalent NWI categories based on the modal NWI water regime associated with each NWI class. Methods were developed for converting the WWI digital databases to make the two inventories more compatible; recommendations for future updates of the WWI include use of leaf-off color infrared aerial photography and merging of the digital WWI with a digital database of deepwater habitats.