EMS was commonly used to induce mutations for various organisms, causing nucleotides to mispair with their complementary bases. So, chemical mutagenesis has become the best method for inducing mutations in genetic studies. Simple PCR-based detection and high-throughput technologies helped to screen and identify mutations. Degenerate oligonucleotide primed PCR (DOP-PCR) became getting attention for mutation survey because the requirement of sequence information and high cost for designing primers could be diminished. Also, high-throughput sequencing instruments, such as GS-FLX, allowed characterization of nucleic acids and massive mutant analysis. A total of 6,696 aligned pairs for Sinpaldalkong 2 vs. SS2-2 and 6,935 for Sinpaldalkong 2 vs. 25-1-1 were formed for mutation detection. A mutation every 437 bp in SS2-2 and every 402 bp in 25-1-1 was observed. About 2/3 of a total of mutations were single base variation in both comparisons. Mutated and non-mutated fragments from SS2-2 and 25-1-1 were distributed on all LGs. The 25-1-1 had more mutations than SS2-2 compared with their wild type, Sinpaldalkong 2. Local compositional bias was also observed around the mutated G. Our modified DOP-PCR primers were successfully amplified and their amplicons were located on randomly but somewhat targeted regions of soybean genome.