Abstract: To investigate the genetic and phylogeography structure of Artemisia intramongolica,which was animportant sand-fixing plant in Hunsandak sandy land in China,the homologous single-copy nuclear genesc9065 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 457bp,respectively,with 14 and 19 variable loci,and 48 and 40 haplotypes were obtained.Based on c9065 andc7847,the haplotype diversity（H_d）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 above0.005,indicating that both species and populations had high genetic diversity.The results of AMOVA analysisshowed 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（N_m）of 6.810 and 7.270,respectively,much greaterthan 1,indicating that there was extensive gene exchange among populations of A.intramongolica.Based onc9065,N_st＜G_st,although N_st＞G_stby 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 Dvalues for both nuclear genes were all not significant（P＞0.05）,while Fu’s F_s values were all significant（P＜0.05）,and combined with the mismatch distribution analysis,A.intramongolica experienced limited populationexpansion under the neutral mode.