Flax (Linum usitatissimum L.) is an economic crop with multiple utilization value. The rich nutrients and active substances of flaxseed as well as high-quality fiber make flax more and more popular. Therefore, producing high-quality flax varieties has become the current breeding goal. Traditional breeding methods have the limitation of the long cycles and limited choices. With the development of molecular biology and molecular markers, the traditional breeding methods combined with molecular breeding have met the breeding requirements. This article reviews the advances made in the application of molecular markers in flax, construction of genetic linkage maps, quantitative trait loci positioning, resistance and fertility marker positioning and genome-wide association analysis. The current problems of molecular marker assisted breeding in flax are discussed to provide some references for flax breeding in the future.