The invention discloses SNP markers closely linked with a height trait of cabbage type rape, and application of the SNP markers. By using an EMS induced mutation technology, a dwarf mutant DF09 with the plant height being 65 cm is obtained. The dwarf mutant DF09 is taken as a research material, a method of map-based cloning is adopted, and a dwarf trait control locus BnDwf.C9 is subjected to finemapping in the 132 Kb interval of a C09 chromosome. In the fine mapping interval, three SNP molecule markers of BnaC09-42, BnaC09-46 and BnaC09-54 which are closely linked with a dwarf trait are obtained. According to the SNP markers closely linked with the height trait of the cabbage type rape, and application of the SNP markers, through a five primer amplification blocked mutation system technology (the BnaC09-42, the BnaC09-46 and the BnaC09-54) or a conventional PCR amplification technology (BnaC09-46pcr), a dwarf material can be accurately screened according to gene types, thus the dwarfmaterial is applied to molecular identification of early target traits, the progress of dwarf breeding is accelerated, and a foundation is laid for clone of dwarf genes.