In the process of regional test and approval of new rice varieties at all levels in China, the consistency of the varieties over testing years and the differences between testing varieties and already approved varieties are mainly judged according to the “Protocol for identification of rice varieties-SSR marker method”. Since the study of rice genome was still in its infancy, the development of these SSR markers was mainly determined based on the results of polymorphism analysis of limited rice varieties, hence there is a lack of sufficient understanding of the 48 SSR markers in terms of their validity and scientific soundness as the basis for distinguishing varieties.This study pinpointed the specific locations of these 48 SSR markers in the rice genome through primer sequence alignment analysis, aiming to explore the distribution patterns of these SSR markers on the rice genome and assess the potential biological effects of their variations. We amplified the public genome assembly data using SSR marker primers and determined the polymorphism of these markers in the indica and japonica rice subspecies groups by analyzing the amplified sequences. The results showed that these 48 markers were unevenly distributed across the 12 chromosomes of rice. Of these, 35 markers were located within genes or within 2.0 kb upstream or downstream of genes, and 3 markers were directly located in the exon regions of genes. However, it is noteworthy that the increase or decrease in SSR repeat units did not lead to frameshift mutations. Among the 193 Asian representative cultivated rice varieties analyzed, 3 markers showed no polymorphism in the japonica group (including 58 varieties), with a polymorphism information content (PIC) of 0; another 8 markers had very low polymorphism in the japonica group (PIC<0.25). Similarly, in the indica group (including 135 varieties), 5 markers also had very low polymorphism (PIC<0.25). In addition to repeat units, single nucleotide variations, as well as insertions and deletions, were observed within the amplified segments. This study not only revealed the genomic characteristics of these 48 SSR markers but also clearly pointed out that a few SSR markers still lack sufficient variety identification capability in representative populations. At the same time, we discovered nucleotide variations beyond the internal repeat sequences of SSR markers, which provides important directions and insights for optimizing existing SSR markers, developing new SSR markers for rice variety identification, and scientifically understanding the limitations of existing SSR markers in variety differentiation.