Aim A surprising finding of genetic studies of Phragmites australis is that native populations, whether in Europe or North America, are characterized by lower genetic diversity than non-native populations. What is not clear is whether higher diversity within invasive stands results from disturbance facilitating sexual reproduction or whether individuals with higher diversity have greater invasion potential.Location Upper Midwest, United States, North America.Methods To answer this question, we investigated genetic structure of native and non-native P. australis stands at multiple spatial scales and under differing levels of anthropogenic disturbance. Our goals were to assess the influence of habitat disturbance on genetic structure and determine whether patterns differed in native versus non-native stands. We also screened for hybrid genotypes, which have not been reported from this region.Results When controlling for disturbance, native and non-native P. australis exhibited relatively similar within-site genetic diversity and degrees of clonal growth, suggesting that their spread is comparably reliant on clonal versus sexual dispersal. In all cases, discrete clumps of P. australis were composed of multiple, closely related genotypes, indicating seed heads as the key dispersal units. The genetic structure of P. australis stands did not differ with disturbance; however, only non-native P. australis was found in highly disturbed anthropogenic habitats. Native P. australis stands exhibited lower genetic diversity overall, lower sexual reproduction in less disturbed sites and greater isolation by distance and differentiation among sites, which is consistent with its longer residence time in this region. We found no evidence of hybrid genotypes, despite native and non-native stands sometimes co-occurring.Main conclusions Our results suggest that invasion by non-native P. australis is sporadic, associated with disturbance and involves closely related individuals, likely derived from a single seed head. The ability of the non-native lineage to exploit a variety of anthropogenic habitats helps to explain its invasiveness.