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The allelic variation in the high molecular weight glutenin subunits (HMW-GS) of 30 Iranian wheat cultivar (T.aestivum L.) was determined by SDS-PAGE technique. Using Laser Scanner densitometiy the area under the peaks was calcuated for the HMW-GS, LMW-GS and w-gliadin. Similarity percentage was calculated using methods such as pearson product, Veinstein, Canbera distance and Euclidean distance. Several dendrogram were classified on the basis of similarity matrix or distance matrix. Different cluster analysis methods (UPGMA,WPGMA,SL and CL) were used for the loci controling the HMW-Glutenin. The optimum result was obtained by UPGMA method