Molecular markers are useful to confirm the hybridity of F1 plant derived from cross of two homozygous parents with similar morphological traits. RAPD markers were used to test F1 hybrid plant obtained from cross of two homozygous soybean (Glycine max) parents. Fl plant for cross I was made from the mating of Hobbit87 (female) and L63-1889 (male) and Fl plant for cross II was obtained from the mating of H1053 (female) and L63-1889 (male). Selfing plant per each cross was also obtained. Among 20 Operon primers used, OPA04 and OPA09 show polymorphism between cross I and II parent. Band in size 1Kb of OPA04 and 2.1Kb of OPA09 primer was polymorphic band. This fragment identified Fl hybrid plant and selfing plant in cross I and II. Female parent Hobbit87 in cross I and H1053 in cross II has no this fragment (recessive allele). However, male parent L63-1889 and Fl hybrid plant in cross I and II has this size of polymorphic band (dominant allele). This indicated that Fl hybrid and selfing plants were detected by RAPD marker before phenotypic marker would be used to identify Fl hybridity. Amplification products of selfing plant for cross I and II were completely same to the those of female parent. When mature, flower color of Fl hybrid plant in cross I and II was purple and flower color of selfing plant in cross I and II was white. Purple flower is dominant trait. Fl hybridity was successfully detected at very early growth stage using RAPD marker. Therefore, RAPD marker can be used broadly to confirm Fl hybridity in many crops.