Abstract: SSR-containing soybean DNA loci useful for genotyping between at least two varieties of soybean. Sequences of the loci are useful for designing primers and probe oligonucleotides for detecting SSR polymorphisms in soybean DNA. SSR polymorphisms are useful for genotyping applications in soybean. The SSR-containing loci are useful to establish marker/trait associations, e.g. in linkage disequilibrium mapping and association studies, positional cloning and transgenic applications, marker-aided breeding and marker-assisted selection, hybrid prediction and identity by descent studies. The SSR markers are also useful in mapping libraries of DNA clones, e.g. for soybean QTLs and genes linked to SSR polymorphisms.