Bean pod mottle virus (BPMV) is a beetle-transmitted virus that can significantly reduce the seed quality and seed yield of soybean, Glycine max (L). Merrill. The simple sequence repeats (SSRs) diversity of 48 soybean genotypes known to differ in their partial resistance to BPMV was evaluated. The objective was to identify genetically diverse parents for developing mapping populations and backcross lines for improving partial resistance of soybean cultivars to BPMV. Two hundred seventy one SSR loci from 87 primer pairs were scored on 48 genotypes (6 U.S. cultivars and 42 plant introduction from China and Japan) using a high-resolution agarose gel screening protocol. The cluster analysis and multidimensional scaling plot were performed using the NTSYS and SAS software, respectively. The cluster analysis revealed two main clusters with eight sub-groups. The genotypes clustered together by their country of origin as well as by their level of partial resistance to BPMV. A number of soybean plant introductions with high-level of partial resistance to BPMV were found to be genetically diverse. This study will allow selection of desired parental combinations for developing mapping populations and breeding lines for improving the partial resistance of soybean to BPMV.