Abstract: In recent years, due to the rapid development of molecular biology and bioinformatics, molecular marker technology based on DNA level can reveal the genetic characteristics of cotton. Molecular markers are based on mutations in DNA base sequences. Compared with morphological, cytological and biochemical markers, this marker has high accuracy, large number and high polymorphism. It has the advantages of good co dominance, no influence on phenotype, simple and rapid detection method, low development and application cost. Molecular marker technology has unique advantages, which can be used to construct genetic map of cotton, molecular marker assisted breeding, marking and positioning of important agronomic traits. It has great practical value in the separation, purification and genetic diversity of germplasm resources. This paper introduces the molecular marker technology applied in cotton fiber in recent years and its application and prospect in cotton breeding.