Phragmites australis is a cosmopolitan clonal species, but one haplotype from Eurasia has become highly invasive in North America. This article describes an investigation of the phylogeographic composition of 77 populations from China, based on the sequencing of two chloroplast non-coding DNA regions. A total of 11 haplotypes were detected, based on the sequence alignments of two chloroplast DNA fragments from 421 sampled individuals. Six of these haplotypes were completely new, and did not correspond to any of this species’ 27 previously known haplotypes. The invasive haplotype M and haplotypes O and P were shown to occur frequently. Haplotype O is widely distributed across all regions and probably represents the primitive haplotype of this species. In contrast, P is mainly distributed in the humid eastern and northeastern regions of China, whereas M is more frequent in western and northwestern China—arid habitats with low precipitation. Between eastern and northeastern and western and northwestern regions, there was distinct genetic differentiation; the former region has a higher genetic diversity than the latter. The high occurrence of haplotype M in western China suggests that it prefers more arid habitats. These findings shed new light on the native distribution, adaptation, and habitat preference of haplotype M, which invaded North America.