Abstract: In order to estimate the level of genetic diversity of Japonica rice in Ningxia, the genetic diversity of sixteen phenotypic characters of the sixty Japonica rice varieties of Ningxia Province were analyzed. The results indicated that, among the sixteen phenotypic characters of the sixty Japonica rice varieties of Ningxia Province had the significant genetic deference, and six phenotypic characters of plant height, total grains per panicl, filled grains per panicl, economic factors, seed setting rate and culm length had bigger variation range and higher vaiance and standard deviation and higher discrete degree; and the coefficient of variation of total grains per panicl, filled grains per panicl, spikelet density, panicles per plant and yield per panicl had over 14%, and F test showed that the sixteen phenotypic characters had extremely significant difference; analyses of genetic correlation showed that among different phenotypic characters had significant and extremely significant correlation, and some of them had positive correlation and some of them had negative correlation, and among different phenotypic characters had complex relationship; analyses of genetic diversity indicated that phenotypic genetic diversity index ranged from 1.644 to 2.092, the average range was 1.957; using chi-square distance by UPGMA clustering method, on the chi-square distance of 0.11 could be classed into eight distinct classes, which the Yanghe white rice, ‘Fu 105’, ‘Tianfeng 302’ and ‘Hua86’ belongs to each class, other germplasms from Ningxia and other provinces had been clustered the Ⅳ, Ⅴ, Ⅵ, Ⅷ class, but 57% germplasms had been clustered the Ⅵ class, and on the chi-square distance of 0.18 the Ⅳ, Ⅴ, Ⅵ, Ⅷ class could be classed into one class, indicated that these germplasm had the close sibship. Yanghe white rice was the landrace of Ningxia and had the farthest genetic relationships than the others. The results showed that, among the Japonica rice varieties of Ningxia Province had lesser genetic difference and single genetic background and closer genetic relationship.