To address the role of polyploidization in grass diversification, we studied Phragmites australis with intraspecific variation of chromosome numbers ranging from 2n=36 to 144. . A combined analysis of genome structure, phylogeny and population genetics were used to study the evolution of P. australis. Genome-wide analysis of 88 individuals collected from different populations around the world and sequenced using restriction site associated DNA sequencing (RAD-seq) identified seven main intraspecific lineages with potential genetic admixture.