The genetic uniformity of six rice cultivars was assessed by 20 SSR markers in this study. In all 21 loci detected, 18 and 11 loci were polymorphic between and within cultivars, respectively. There were two types of non-uniformity within cultivars, the overwhelming one was the type that had more than one homozygote in a locus, and the other one was heterozygote. Results of principal coordinates analysis and cluster analysis showed that the cultivars were uniquely identifiable in spite of the non-uniformity detected within each cultivars. Based on the level of non-uniformity obtained in this research, we recommended using 0.1 as the acceptable upper limit for averaged genetic distance among variants within a cultivar. The effects of genetic non-uniformity based on molecular markers on variety identification and Plant Breeder's Right were also discussed.