The common reed, Phragmites australis, is a common feature in wetlands across North America. Recent studies have suggested that the widespread invasions of this species may be due to the introduction of a non-native strain from EurAsia. Since native populations persist in many areas where introduced populations are also found, a method for distinguishing population types is needed to facilitate management of the species. A restriction fragment length polymorphism (RFLP) assay was developed to distinguish native, non-native, and Gulf Coast type populations of Phragmites from each other. Two amplified non-coding chloroplast DNA regions are each cut with one restriction enzyme, allowing the distinction of native, non-native and Gulf Coast haplotypes from each other. When used together, these cut sites provide a low cost, rapid way of determining the origin of Phragmites populations.