Over the past several decades, populations of the common reed, Phragmites australis, have expanded rapidly in salt marshes of coastal North America, creating dramatic changes in community composition. Populations of Phragmites in coastal wetlands of the Great Lakes may similarly threaten the ecological integrity of these inland wetland communities. Strategies for the conservation of biodiversity in these wetlands should be informed by an understanding of both the recent trends and the historic role of Phragmites in these wetlands. A combination of paleoecological and genetic analyses was used to determine when Phragmites became established in a Lake Superior coastal wetland and whether the source of Phragmites was native or non-native populations. Radiocarbon-dated stratigraphic changes in the abundance of pollen and macroscopic plant remains were used to infer the timing of vegetation changes in the wetland. From about 1100–490 ¹⁴C yr ago, low water levels were associated with a lowland conifer forest with wetland swales at this site. At about 490 BP, conifers became less common, and peatlands became established at the site, perhaps in response to higher water levels in the wetland. There is no evidence that Phragmites grew at the site until the last several decades, suggesting that it is not native to this wetland and that its recent expansion may create significant changes in the wetland community. However, genetic data from chloroplast DNA sequences and microsatellite markers indicate that it is a variety that is native to North America and common throughout the Midwest. Our results suggest that human-induced changes in the landscape in combination with long-term environmental changes may play an important role in the expansion of native Phragmites populations.