Abstract:Genetic diversity in 144 accessions of upland rice germplasm from 4 geographic regions was assessed using 38 pairs SSR markers. A total of 137 alleles were detected ranging from 2 to 9 per locus with the mean of 3.6. The Nei’s gene diversity indices (He) ranged from 0.440 at RM162 to 0.854 at RM335, with the average of 0.598. There existed significant difference in SSR allelic diversity between indica and japonica subspecies. Indica upland rice（Na = 3.5, He = 0.558）had more variation than japonica one (Na = 3.2, He = 0.415), revealing the gene diversity of indica upland rice was more exuberant than that of japonica one. Regarding geographies regions, the He of upland rices in Asia countries (except China) was the highest, the followings were that in China (He 0.593), in South America (He 0.545) and in Africa (He 0.512). The analysis of molecular variance (AMOVA) indicated that 76.3% and 23.7% of total genetic variation were existed within subspecies and between subspecies with significant difference at 0.001 probability level respectively, showing the most genetic variation of upland rices came from within subspecies. Based on Nei’s genetic distance using data of 38 SSR loci, 144 upland rice germplasm could be distinguished as indica and japonica, but not be classified better into groups according to geographical regions. The present study verified that upland rices have rich genetic diversity, which is an excellent basis for upland rice breeding for tolerance to water stress.