In this article, 38 example varieties and 52 basic characteristics in rice DUS testing guideline were used to evaluate the genetic diversity of 172 varieties of japonica rice landraces from shanghai region. 14 modern cultivars from the same region were compared with these landraces for finding their relationship. The result showed that there were totally 176 alleles, 3.6667 alleles per characteristic with range from 1 to 8 in morphological characteristic of landrace. The Shannon’s diversity index (H’) of landrace was 0.6834 on average, ranged from 0 to 1.9327. Almost 77.08 percent of all the characteristics had more than three alleles. The genetic diversity of landrace was higher than the modern cultivars according to comparing their total alleles, alleles per characteristic and H’ value. All the varieties could be well divided into 3 groups with one group containing all the modern cultivars at a genetic similarity coefficient of 0.53 with UPGMA clustering analysis method, and into two distinguished areas with principal coordinates analysis method. Japonica rice landraces from shanghai have rich diversity, with great differences to modern cultivars on these morphological characteristics, which can be good utilized in japonica rice breeding improvement in future.