Abstract: Simple sequence repeat (SSR) molecular marker was used to analyze the frequency of polymorphism of wheat varieties – Flinor and Mingxian169. The result was followed. Of 1243 SSR markers used to investigate DNA polymorphism of the two cultivars, 383 markers could express the polymorphic and cover 31.10%, 127 markers had no clear band, and 733 markers had no polymorphic and covered 59.35%. The polymorphism of BARC, WMS and CFA was higher with 34.98%, 34.72 and 36.49, respectively, while the polymorphism of CWEM was lower with 8.89%. The distribution frequency of polymorphic markers was different among the chromosome in the A, B and D genome, the highest in A genome (41%), lower in B genome (35%) and the lowest in D genome (24%).