Powdery mildew, caused by Blumeria graminis f.sp. tritici (Bgt), is one of the most important wheat diseases worldwide．Common wheat line ND399, with pedigree Torino/2*2552// 9516/3/5*Shi4185, is a new registered high-yielding and powdery mildew resistance cultivar. Genetic analysis using an F2 segregating population and F2:3 families，originally from a cross between susceptible line Shi4185 (IT: 4) and ND399 (IT: 0;), indicated that a single dominant gene, temporarily designated MlND399, confers powdery mildew resistance in ND399 at seedling stage．By applying molecular markers and bulked segregant analyses (BSA)，a polymorphic SSR marker (Xcfd81 ) and two AFLP-derived SCAR markers (SCAR203 and SCAR112) were found to be linked to MlND399．Among these markers, Xcfd81, SCAR203 and SCAR112 were linked to MlND399 with genetic distances of 0.2cM, 1.0cM and 1.2 cM, respectively．MlND399 was physically located on chromosome 5DS bin 0.67-0.78 using Chinese Spring nullisomic-tetrasomic and deletion lines．According to the infection type of MlND399 to Bgt isolate E09 and molecular marker mapping results, MlND399 was supposed to be powdery mildew resistance gene Pm2．These molecular markers linked to MlND399 provide useful tool in pyramiding and maker assisted selection of the powdery mildew resistance gene in ND399.