Genetic diversity of 36 genotypes of dwarf and semi-dwarf apple rootstocks along with seven Iranian dwarf rootstocks were investigated by use of RAPD DNA markers. A set of 100 random primers was utilized in PCR reaction from which 10 primers resulted in good amplification with high polymorphism. Among primers, 10 selected RAPD primers produced 160 bands, in which, 136 were polymorphic. Cluster analysis was done based on polymorphic bands using Dice similarity coefficient and UPGMA method. The highest genetic similarity (90%) was detected between B9a and B9b samples. Grouping of dwarf apple rootstocks showed the most proper correlation with their sampling area, showing either close genetic background or existence of the same parents. In cluster analysis, four distinct groups of 0.6 similarities were identified. Cophenetic coefficient between similarity matrices and dendrogram was 0.89, showing a proper fit of dendrogram with similarity matrices. This experiment showed RAPD markers as a suitable and efficient technique to differentiate apple Dwarf rootstock samples.