In order to clarify the genetic basis of rice varieties bred in the three provinces of Northeast China in recent years, 20 materials were selected as the breeding core parents by analyzing the pedigree of 256 approved rice varieties which bred in 2021. And 44 SSR polymorphic markers and 34 InDel xiangeng specific markers were used to analyze on their genetic diversity and xiangeng differentiation. The results showed that: (1) all selected markers can be applied extensively for the genetic diversity level of rice. A total of 130 alleles were detected between these varieties, and the alleles (Na) per locus ranged from 2 to 5 with the mean value of 2.95. The gene diversity indices (H) varied from 0.10 to 0.75 with an average of 0.41. The polymorphism information content (PIC) was changed from 0.09 to 0.70 with the average of 0.36. (2) Genetic diversity analysis showed that the overall diversity level of the test materials in Northeast China at a lower level, and the diversity of the core parents in Heilongjiang was slightly higher than that in Liaoning and Jilin. (3) The NJ cluster analysis indicated that all tested materials could be divided into three groups, such as Liaoning group, Jilin group and Heilongjiang group. (4) The genetic structure analysis showed that the 20 core parents could be divided into two stable groups. The core parents of Liaoning Province were in group A, and the core parents of Heilongjiang Province were in group B. (5) Analysis of xiangeng differentiation found that the 20 materials were geng type, but all of these materials contained a few number of xian loci, and the xian gene frequency (F_x) range was 0.01-0.19. Studies have shown that the possible reasons for the low level of genetic diversity of breeding varieties is the narrow genetic basis and high utilization frequency of breeding core parents in the three provinces of Northeast China. It is urgent to excavate new germplasm, introduce new resources in breeding to broaden the genetic background.