Soybean cyst nematode (SCN) (Heterodera glycines) has been one of the most destructive pests of soybean in the USA. Using cultivars with resistance to SCN is the most effective strategy to manage the pest. Cultivars with SCN resistance have been developed and used in soybean production. However, only a few SCN resistant sources have been deployed in the USA. These resistant cultivars face challenges of being overcome by SCN. Over 100 SCN resistant sources have been identified from the USDA Soybean Germplasm Collection. Little is known of the genetic relationships among these SCN resistant sources. The objectives of this research are to evaluate genetic variation and determine the genetic relationships among SCN resistant sources. One hundred and twenty-four genotypes have been evaluated by simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) marker. Eighty-eight SSR markers from 20 linkage groups and 44 RAPD markers are employed. Nonhierarchical (VARCLUS) and hierarchical (Ward's) clustering are combined with multidimensional scaling (MSD) to determine relationships among tested genotypes. AMOVA methodology is used to evaluate genetic variation.