The genus Sesbania Scop is one of the important genera of the family Fabaceae and is well-known for being highly promising green manure crops. Crop improvement for increased utilization of the members of this genus can be done with the help of conventional and molecular breeding programs for which the assessment of genetic variability is a pre-requisite. In this study, twelve accessions representing five species of Sesbania Scop are studied for their genetic diversity. The DNA was isolated from fresh leaf samples and analyzed by using eight Inter Simple Sequence Repeat primers using Polymerase Chain Reaction and Electrophoresis techniques. Analysis of the band statistics and efficiency parameters of the primers is done after obtaining the DNA banding patterns. The total number of bands amplified are 79 of which 76 are polymorphic indicating a very high degree of genetic variability. The overall percentage of polymorphism observed was 96.2%.Jaccard’s similarity coefficients are calculated and the highest similarity value of 0.895 is seen between the two accessions of S2 (S. sericea (Willd.) Link IC0631284) and S3 (S. sericea (Willd.) Link IC0635936).Principal Component Analysis and Dendrogram analyses grouped all the twelve accessions into 2 major clusters and 5 sub-clusters.Based on the genetic variability, the most useful germplasms for breeding programs are found to be S2 (S. sericea (Willd.) Link IC0631284) , S5 (S. grandiflora (L.) Pers. IC0564742 ) and S6 (S. aculeata (Willd.) Pers. IC0445741). The exclusive clustering of S.grandiflora accessions was observed in addition to the grouping of accessions based on their biological statuses.