In this research, the 4 retrotransposons that belong to Oryza, including active, low copy number: Tos17/Osr21 (Ty1copia) and RIRE7/Osr31 (Ty3gypsy); inactive, high copy number: Osr34 (Ty3gypsy) and Houba/Tos5/Osr13 (Ty1copia). Were used to design primers form the long terminal repeat region (LTR) of the two lateral wings. In the mean time, PCR amplifications were carried through to 37 Oryza sativa L. ssp. japonica cultivated varieties (strains) in Xinjiang. Rice LTR retrotransposons that applies to the interretrotransposon amplified polymorphism (IRAP) markers were evaluated and identified, and the genetic diversity of 37 varieties (strains) were analyzed. (1) The results of PCR amplification showed that Tos17/Osr21, RIRE7/Osr31, Osr34 and Houba/Tos5/Osr13 were in turn obtain 73, 63, 107 and 560 bands, of which polymorphic bands were 36, 63, 70 and 523, the polymorphic rate was 49.3%, 100.0%, 65.4% and 93.4%, respectively. (2) Comprehensive evaluation and comparison polymorphism, heterogeneity, the total number of bands and the average number of polymorphic bands, indicated that Houba/Tos5/Osr13 is suitable for the IRAP marker method to construct the DNA fingerprint database. (3) Based on the genetic similarity coefficient of Houba/Tos5/Osr13, clustering analysis through unweight pair method using arithmetic averages (UPGMA) method. According to 0.55 threshold value that 37 O. sativa L. ssp. japonica cultivated varieties (strains) in Xinjiang were divided into 6 groups, and most of the varieties (strains) have been clearly distincted. The genetic similarity among varieties was high, and the degree of diversification was low. The strains ‘2018’ and ‘9616’ were clustered into separate classes, indicating that the genetic background between cultivars and varieties is far away and the degree of diversification is high. In summary, IRAP molecular marker was suitable for genetic relationship analysis of O. sativa L. ssp. japonica germplasm resources in Xinjiang, identification and determination of genetic distance of breeding, the construction of DNA fingerprint database as well as the research of related fields. In the actual breeding, different varieties and strains of rice were selected for cross breeding, the success rate was high, which could greatly shorten the breeding process of fine varieties.