In order to analyze variation and find an efficient selection approach, we used crossing results between two wheat cultivars, Azar2 and 87-Zhong291. F3 plants (374 lines) and four check cultivars planted in the form of augmented experiment. For germination, seeds were irrigated once. After using multiple statistics methods such as cluster analysis, 79 different lines were selected and used for RAPD analysis with UBC3 primer that hadproduced six polymorphic bands (447 fragments in total). Jaccard's coefficient for parents was low (0.17). Therefore, Azar-2 and 87-Zhong291 had extreme differences with each other. For the analysis of relationship between polymorphic bands and morphological characters, logistic regression was used. The majority of characters were not related to the bands but some of morphological characters, such as biological yield, plant height, main spike weight, 1000 grain weight and peduncle length showed a negative relation with some of polymorphic bands. Among them, seed number/spike trait had a positive relationship with a 600bp band. This band could be used as a selection marker for seed number/spike trait.