The comparision of main agronomic traits of different period rice varieties（strains） commercially grown in Ningxia showed the significant difference of agronomic characters between the first stage (1950 ~ 1962) and the second(1978～1989 year), the third (1990～1999 year),the forth(2000～2005 year), the fifth(2006～2012 year),the six(2010～2013 year) stage. This means that, the agronomic traits of rice varieties in Ningxia was improved by breeding techniques. There was a decreasing trend of effective panicle and a increasing trend of days of growth period, panicle length, spikelets per panicle, weight per panicle, weight per plant, and grain yield per unit area from the second stage to the sixth stage were found. The pattern of breeding of grain yield traits become to panicle weight type or both of panicle and spikelet type from panicle number type. The analysis of the genetic diversity of 76 rice varieties bred in different period of Ningxia was analysedby using 48 polymorphic simple sequence repeats (SSR) markers shows that there was total of 290 alleles were detected, and the number of alleles per pair of primers ranged from 3 to 15 with a mean value of 6.04. Among which, 109 alleles (37.59%) were minor alleles. RM333、RM297、RM249、RM501 and RM206 showed higher score of alleles and minor alleles, which were suitable to assess the genetic diversity of rice varieties from Ningxia. Polymorphic information content (PIC) was ranged from 0.1423 to 0.8783 with a mean value of 0.5512. The Nei’s genetic diversity index (He) was ranged from 0.1492 to 0.8945 with a mean value of 0.6032. The results of analysis of molecular variance (AMOVA) indicated that the genetic variation among the six decades stages was just only accounted for 19.27% of the total genetic variation, but which the genetic variation among the variety varieties within during every decade stage was accounted for 80.73%. The UPGMA cluster analysis of 76 rice varieties in Ningxia showed that there were five categories were clustered in the 0.805 level of genetic similarity coefficient. Twelve rice landraces were clustered into the Ⅰ group; the Ⅱ group included eight conventional japonica rice varieties, which had blood relationship with foreign varieties; the Ⅲ group included five high quality rice improved varieties; the Ⅴ group included two large-panicle and high-grain yielding improved cultivars. 49 conventional japonica rice varieties were clustered in the Ⅳ group, it showed that majority rice varieties in Ningxia had a closer genetic relationship. The UPGMA cluster analysis of six stages of rice varieties in Ningxia showed that , the first stage (Landrace) was clustered into a separate category , it has a relatively low genomic affinity to others. The relationship was relatively distant between the second, the third, the forth stage and the fifth, the six stage. The results of genetic diversity analysis of different period rice varieties in Ningxia showed that there was greater differences of genetic diversity betweenamong the six different periods, and the genetic diversity decreased after 2005. In order to accelerate the rice breeding process in Ningxia, we should strengthen the introduction and use of rice germplasm resources from other provinces and abroad, and to explore the favorable genes from rice landrace and weedy rice in Ningxia, to and broaden the genetic basis of in order to improved the rapid development of rice breedingcultivars in Ningxia.