Tamarix chinensis Lour. is a perennial shrub that is highly adapted to flooded and salty conditions with a wide distribution. In this paper, a phylogeographic history of T. chinensis including 20 populations from China was inferred using two chloroplast DNA (cpDNA) segments (trnL-trnF, and rps16) and one nuclear ribosomal DNA (nrDNA) region. A total of 11 ribotypes and 16 chlorotypes were identified. The total nucleotide diversity (H_T) of the nrITS and cpDNA were 0.803 and 0.635 respectively, showing a moderate level of genetic variation. The haplotype trees of both nrITS and cpDNA exhibited an H1-centred radiation differentiation pattern. In addition, both cpDNA and nrITS data showed no significant population differentiation within T. chinensis. AMOVA results revealed that almost all genetic variations existed within the populations. Furthermore, we found relatively stronger population differentiation based on nrITS rather than that of cpDNA. nrITS indicated a significant positive correlation between the genetic differentiation coefficient and geographic distance. These results implied that seed dispersal is more efficient than pollen dispersal in T. chinensis. The molecular data and ecological niche modelling also indicated that T. chinensis retreated into refugia on a large-scale during the Last Glacial Maximum (LGM) period and then there was sudden population expansion and recolonisation of suitable habitats after the glacial period.