Abstract: Study on the genetic diversity, genetic structure, genetic specificity and the relationship of different rice populations in Asian ecological areas can provide genetic basis for exploring rice origin and selecting parental materials. 119 pairs of SSR markers which distributed in 12 chromosomes were selected, and the whole genomes of 440 rice cultivars were scanned. The genetic diversity and genetic structure were analyzed by PowerMarker 3.25 and Structure 2.2. A total of 781 alleles were produced in Taihu Lake rice cultivars and the PIC average value was 0.52. A total of 295 alleles were produced in Heilongjiang rice cultivars and the PIC average value was 0.25. A total of 370 alleles were produced in Vietnam rice cultivars and the PIC average value was 0.30. It indicated that the genetic diversity of Taihu Lake rice was higher than that of Vietnam and Heilongjiang rice. Heilongjiang rice population had the most specifically deficient alleles (132) and the Taihu Lake subpopulation had the least (4). The Taihu Lake rice population had the most specifically existent alleles (284) and Heilongjiang rice population (25) had the least. The Taihu Lake subpopulation had the most complementary number of alleles (447) for Heilongjiang subpopulation. The Heilongjiang subpopulation had the least complementary number of alleles (29) for Taihu Lake subpopulation. The 440 varieties in the three regions were divided into seven germplasm groups by Structure 2.2, they were not independent but interpenetrating. The genetic background of rice cultivar populations in different Asian ecological areas has integration and complementation, which could widen the breeding resources.