Genetic diversity and reproductive mode can control whether an introduced species becomes invasive. Here we use genetic tools to compare the non-native, invasive Phragmites australis to its native conspecific, P. australis subsp. americanus, in wetlands of Utah and southern Idaho. We found striking differences in genetic structuring, population diversity, and mode of reproduction between the two lineages. Non-native P. australis exhibited substantially more genetic homogeneity among populations, greater local genet richness, greater genetic diversity among individuals, and smaller average clone size compared to the native lineage. These findings suggest that non-native P. australis relies more heavily on sexual reproduction and disperses pollen and/or seeds more widely than native P. australis. We also found no evidence of hybridization between the two lineages, nor did we find evidence of local extirpations of native by non-native P. australis based on historical collection sites we revisited. Given the ability of non-native P. australis to disperse widely by seeds, we recommend careful monitoring of critical wetland habitat to detect new non-native P. australis invasions and incorporating new practices into Phragmites management that limit sexual reproduction.