ABSTRACT Calligonum is the only C4 genus within Polygonaceae. We applied DNA sequences from the nuclear ribosomal internal transcribed spacer (nrITS) and five plastid genome regions (psbA-trnH, ycf6-psbM, trnL-F, rpl32-trnL and rbcL) to reconstruct the phylogeny of Calligonum. The nrITS and the combined plastid DNA regions were analysed separately. The phylogeny of the five plastid genome regions supports the treatment of the Calligonum mongolicum complex as a single species with intra-specific geographic structure, and suggests independent hybrid origins for the polyploid species C. caput-medusae and C. arborescens through comparisons with the nrITS tree. We detected phylogenetic incongruence between the nrITS and plastid DNA trees and hypothesized reticulate evolution or hybrid speciation in the genus. Divergence time dating based on nrITS determined that the most recent common ancestor of Calligonum species began diversification 3.46 million years ago [mya; 95 % high probability density (HPD): 1.87-5.71 mya], and diversification began in the Central Asia and China clade ca. 2.68 mya (95 % HPD: 1.28-4.59 mya). We expect that future studies employing next generation sequencing methods, such as RAD-seq, coupled with denser inter- and intra- specific taxonomic sampling, may prove to be cost-effective methods for further investigation of the evolutionary history of this genus.