Various studies showed that the genetic diversity in soybean (Glycine max) germplasm is limited. There is insufficient data on molecular analysis of soybean collections from Africa. The main objectives of the present study were 1) to analyze the genetic diversity and relationships among soybean accessions identified in DR-Congo gene pool, and 2) to determine the effect of gamma radiation on genetic variability. The level of polymorphic loci among the soybean varieties was high, varying from 70% to 90% based on ISSR primers used. The soybean varieties analyzed were genetically related with several accessions exhibiting similar ISSR amplification profiles. Seed treatment with gamma-rays at 0.2 KGy (20 Krad) increases the level of polymorphism in progenies. Low genetic diversity observed within varieties was increased with gamma-ray treatment at 0.1 KGy (10 Krad) and 0.2 KGy (20 Krad) dose. The results need to be confirmed with advanced generations derived from gamma –irradiated seeds.