Abstract: Molecular marker technology is one of the most important auxiliary means of cotton genetic breeding, which has made a significant progress in cotton molecular marker breeding research. This article gave an overview of the research progress in analysis of genetic diversity, prediction of heterosis, identification of germplasm, genes mapped and markerassisted selection breeding. In addition, problems appearing in the application process of cottom molecular marker technology would be discussed in order to expect it to be better used in genetic breeding, which would provide more powerful auxiliary means for selecting and cultivating new cotton cultivars that possessed superior multiple traits