Within the genus Phragmites (Poaceae), the species P. australis (the common reed) is virtually cosmopolitan, and shows considerable variation in ploidy level and morphology. Genetic variation in Phragmites was studied using AFLPs, and analysed with parsimony and distance methods. Groups of P. australis strongly supported in the analyses include one that comprises all South American clones, a distinct group from the US Gulf Coast, and a group of E. Asian and Australian octoploids. Among the other species, the paleotropical P. vallatoria is supported as monophyletic and most closely related to the paraphyletic P. mauritianus and to the Gulf Coast and S. American groups. The E. Asian species P. japonicus is closely related to a group of P. australis clones mostly from central North America. Tetraploidy predominates in the genus, and optimisation of chromosome numbers onto the phylogeny shows that higher ploidy levels have evolved many times.