Estuaries are dynamic and selective environments that provide frequent opportunities for the turnover of Phragmites australis populations. We studied Phragmites genetic diversity patterns in three of the major deltas of China, viz. the Yellow River, the Yangtze and the Liaohe, in relation to Phragmites global phylogeography and soil salinity. We found that two distantly related P. australis haplotypes, each with intercontinental distribution, co-occur in these deltas in China. One is European Phragmites (Haplotype O) and is related to P. japonicus; the other (Haplotype P) has its range in East Asia and Australia and is related to the Asian tropical species P. karka. The two haplotypes have differing salt tolerance, with Haplotype O in areas with the highest salinity and Haplotype P in areas with the lowest. Introgressed hybrids of Haplotype P with P. karka, and F1 hybrids with Haplotype O, have higher salt tolerance than Haplotype P. Phylogenetic diversity appears as the factor that better explains population structure and salinity tolerance in these estuaries. Future research may explain whether the two P. australis haplotypes evolved in East Asia, and East Asia is a center of Phragmites diversity, or are introduced and a threat to P. japonicus and P. karka.