To investigate the genetic and phylogeography structure of Artemisia intramongolica， which was an important sand-fixing plant in Hunsandak sandy land in China， the homologous single-copy nuclear genes c9065 and c7847 were developed by transcriptome sequencing， and then eight natural populations of A. intramongolica were studied. The results showed that the total length of c9065 and c7847 were 485 bp and 457 bp， respectively， with 14 and 19 variable loci， and 48 and 40 haplotypes were obtained. Based on c9065 and c7847， the haplotype diversity（Hd） was 0.871 6 and 0.934 8， respectively， and all populations were above 0.8. The total nucleotide diversity（π） was 0.008 2 and 0.005 9， respectively， and all populations were above 0.005， indicating that both species and populations had high genetic diversity. The results of AMOVA analysis showed that 99.398% and 98.908% of genetic variation existed within the populations of A. intramongolica based on c9065 and c7847， respectively， with gene flow（Nm）of 6.810 and 7.270， respectively， much greater than 1， indicating that there was extensive gene exchange among populations of A. intramongolica. Based on c9065， Nst<Gst， although Nst>Gst by c7847， but the difference was not significant（P>0.05）， indicating that A.intramongolica population did not exist phylogeographic structure. The neutral test showed that Tajima’s D values for both nuclear genes