Abstract: Combination of molecular marker and traditional breeding can identify plant genotype in the early breeding time，it isn’t influenced by environment，also don’t interfered the plant normal growth and development. Molecular marker assisted breeding can greatly shorten the breeding process，improve the efficiency of breeding. This article summaried the research progress of molecular markers and its application in the genetic breeding of rapeseed from four aspects，including genetic map construction，gene location and cloning，molecular marker-assisted selection，and discussed the application of genome，comparative genome research in the map based cloning of Brassica napus，thus to establish the basis for further study.