Wheat is the major nutrient source for numerous people. Aegilops tauschii Coss. (DD), the D genome donor of common wheat (BBAADD), exhibits abundant genetic variations in selenium and zinc concentrations. Ae. tauschii accession AS2407 exhibited prominent Se and Zn accumulation ability. The objectives of this study were to map Se and Zn accumulation-related quantitative trait loci (QTLs) and to identify candidate genes controlling Se and Zn accumulation in Ae. Tauschii. In this study, quantitative trait locus (QTL) mapping was carried out for selenium and zinc accumulation in the aerial parts of recombinant inbred lines (RILs) derived from two subspecies, AS2407 (Ae. Tauschii. ssp. strangulate) and AS65 (Ae. Tauschii. ssp. tauchii), and candidate genes were screened. Kompetitive allele-specific polymerase chain reaction (PCR) (KASP) markers, which are closely linked to QTLs, were developed, and their distributions were detected in a natural population of Ae. Tauschii. QTLs controlling selenium and zinc content were identified on chromosomes 1D and 2D, named QSe-1D and QZn-2D, respectively, which could explain 11.94% and 13.49% of the phenotypic variation, respectively. Five selenium-related candidate genes and three zinc-related candidate genes were screened. KASP markers (KASP_Chr1_22217614 and KASP_Chr2_57200260) were developed. QSe-1D and QZn-2D are the first mapped QTLs controlling selenium and zinc accumulation in the aerial part of Ae. tauschii. These QTLs and KASP markers will be useful for quality improvement of wheat high nutrition and valuable for understanding the biological basis of Se and Zn intake in Ae. Tauschii.