Abstract: Atraphaxis, Calligonum, Parapteropyrum and Pteropyrum are all the genera of Polygonaceae distributed in arid and semiarid areas. The four genera have many similar characters in morphology. In China, Atraphaxis and Calligonum are mainly distributed in Xinjiang, and Parapteropyrum is endemic in Tibet. The genus Pteropyrum including 3-5 species can be found in Southwest Asia and Middle East. Total genomic DNA of Atraphaxis, Calligonum, Parapteropyrum and Pteropyrum was extracted from the leaves dried with silicagel or from herbaria, the polymerase chain reaction (PCR) was used to amplify the chloroplast DNA atpB-rbcL region. The atpB-rbcL , the intergenic spacer between atpB gene and rbcL gene, about 900 bp in length, is widely used for the phylogenetic analysis on generic level. The phylogenetic tree based on the atpB-rbcL sequences reveals that Calligonum shows closer relation to Pteropyrum, additionally, Parapteropyrum is out of the clade including Calligonum, Pteropyrum and Atraphaxis.Within Calligonum,Section Calligonum, Section Medusa and Section Pterococcus formed a small clade, which is distinct from Section Calliphysa.

Key words: Polygonaceae, chloroplast DNA, atpB-rbcL, phylogenetic relation, arid area