The invention relates to the fields of plant genetics and wheat breeding, in particular relates to a molecular marker for a wheat anti-stripe rust character, namely a wheat anti-strip rust gene Yr69 as well as a linked SSR molecular marker and an application method thereof, and aims at solving the problems that genetic distance between an existing molecular marker and the anti-strip rust gene Yr69 is long and marking is not accurate enough. The application method comprises the following steps: 1) amplifying by taking wheat DNA as a template and 2SA33 as a primer; 2) sequentially carrying out pre-degeneration, degeneration, annealing, extending, cycling, extending, and storing for later use; 3) carrying out electrophoresis, then mixing electrophoresis products with a loading buffer solution, then carrying out sample application, carrying out electrophoresis, and then dyeing and photographing; and 4) determining that Yr69 exists if a specific stripe is amplified. The invention has the advantages that firstly, the 2AS33 is obtained; and secondly, a dominant marker is adopted, the genetic distance is 1.9cm, the Yr69 gene is rapidly and accurately identified, powdery mildew resistance is predicted, and utilization of Yr69 is promoted.