Technical Abstract: Korean and Chinese cultivated soybean [Glycine max (L.) Merr.] populations are major soybean gene pools. Information has been reported comparing genetic diversity between soybeans from the two countries using an unequal number of accessions and only 6 to 35 genetic markers. This study compares differences across 49 simple sequence repeat markers covering the 20 soybean chromosomes to assess genetic diversity and genetic relationships among ninety cultivated soybean accessions, each collected over a wide geographical area from Korea and China. Soybean populations from both countries had high genetic diversity indexes (H), but was higher for the Chinese population (H=0.76) than the Korean population (H=0.72). Soybean accessions collected from Central China had the highest genetic diversity value (H=0.73) compared to accessions from regions of Southern and Northern China or Northern and Southern Korea where diversity values ranged from H=0.70 to 0.71. Accessions from Korea showed less molecular variation than accessions from China. Accessions from the two Korean regions grouped closely genetically, but were grouped apart from the Chinese population. Structure and Principal Coordinate Analysis showed that gene flow occurred between the two countries; however Korean and Chinese soybean populations were genetically distinct. Therefore, soybean accessions originating from both countries represent unique gene pools for soybean improvement.