Chinese Spring and its null-tetrasomic lines were used to identify the specific bands of STS-marker and microsatellites (SSR) marker of wx genes. Twelve varieties and five waxy wheat lines were screened with these two markers, and the results are in agreement with those from Wx subunits SDS-PAGE. A F2 segregating population from cross Jiangsu Baihuomai x Kanto 107 was also detected by molecular markers, not only eight wx genotypes were developed while three genotypes did not exist in the nature, but also the first batch of waxy wheat lines were bred. The Jiangsu Bainuomai improvement population was screened, and six 7D momosomic plants with wx-D1b were obtained, which could provide materials for waxy wheat breeding. Application molecular markers of wx genes will improve the selection procedure for the waxy wheat and good noodle-quality wheat.