Pomegranate ( Punica granatum L) is one of fruit bearing trees that have been planted in Iran for many years. Iran is one of the leading pomegranate producing countries in the world and has vast cultivar variation. Knowing all the morphological, physiological, fruit development, fruit size and quality that depends on successful pollination, fruit setting and number of fertilized seeds is essential to have an economical production and reach to the standards of the export markets. There has not been any precise investigation on the mode of pollination of pomegranate in Iran and in the world. Since current methods of studying mode of pollination in pomegranate are not reliable enough, in this research work viability, germination percentage and vigor of seeds and seedlings and efficiency of RAPD, AFLP and ISSR markers were considered. Seeds of four genotypes of pomegranate namely: Maalas e Saveh, Shirin e baft, Dopaye ravar and Pust siah e saaveh were treated with GA (500, 1000 and 1500 ppm), cold and washing and in vitro embryo cultyre was used to speed up germination. Maalas e Saaveh genotype was better than others in germination, growth and root formation, so it was selected to be used in molecular steps. Ten Random primers that had indicated maximum polymorphism in the previous studies were used in the RAPD experiment. Comparison of progenies and maternal RAPD patterns did not show any difference among genotypes. In another experiment the samples were tested with AFLP and ISSR markers but the results were not suitable enough to analyze. Employing different methods for selecting seed like obligatory self pollination and selective cross pollination and using DNA markers with higher capability is suggested.