Molecular markers are useful tool to study genetic diversity and the relationship between genotypes. The evaluation of genetic diversity in species is a start step for breeding program. In this study, molecular markers were used to determine diversity and genetic relationships of 120 kiwifruit genotypes. During two consecutive growing seasons, thirty-two discretional morphological traits were studied by the International Union for the Protection of New Varieties of Plants (UPOV) in new kiwifruit genotypes. Average value of polymorphism per primer was 95.1%. Polymorphism information content values for all the primers used ranged from 0.32 to 0.41. High levels of polymorphism were found for all marker systems. Dendrogram generated using unweighted pair group method with arithmetic cluster analysis based on Jaccard’s similarity coefficient and dendrogram generated using Neighbor-joining cluster analysis accessions were separated 120 genotypes into 11 and 5 groups, respectively. For all markers, 171 marker–trait associations were found with the GLM, the significance criteria defined for the traits only at the P≤0.01 level. This study results provide useful genetic information about new kiwifruit genotypes of Iran and indicate that the use of new kiwifruit genotypes in breeding program could be useful for generating new cultivars with novel characteristics.