Ten genetically stable fusants strains were obtained as a result of protoplast fusion technique between Bacillus sphaericus (Bs) and Bacillus thuringiensis (Bt), six of them produced from, Bs GHAI Bt 66 Ia experiment (fusants no. 1, 2, 16, 26, 31 and 34) and four fusants produced from Bs GHAI Bt I977experiment (fusants no.1, 2, 17 and 25). Two molecular marker systems, four ISSR primers (Inter-Simple Sequence Repeat) and seven SCoT primers (Start Codon Targeted Polymorphism) were employed for detection of genetic variation between the parents and their fusants. Four ISSR primers and seven SCoT detected 55and 97 amplicons, among which 92.696% and 81.948% bands were polymorphic respectively. The genetic similarity values among the species were calculated based on ISSR and SCoT profiles which ranged from 0.50 to 0.83 and 0.59 to 0.90 respectively. Based on the marker analysis, the three parents and the ten fusants were clustered into three major groups for ISSR primer and SCoT primers. Cluster analysis were performed to construct a dendrogram of the Bacillus Strains and their fusants and also reveals high genetic variation among the parents and their fusants. It could be concluded that each type of the two molecular marker approaches of DNA analysis could identify the different between the parents, and all of their fusants under investigation have probably originated from closely related ancestors and possess high degree of genetic similarity.