Leptospirosis is an emerging zoonotic disease with widespread distribution. The disease, caused by a large number of pathogenic serovars of leptospires, varies in severity from mild flu like illness to severe and fatal forms. It has often been observed that the strains of the same serovar are associated with different clinical syndromes. In this study the isolates recovered from patients with mild and severe form of leptospirosis and those isolated from rodents trapped in the same areas were analyzed by using random amplified polymorphic DNA (RAPD) fingerprinting method using the primers PB1, M16, B11 and B12. RAPD fingerprinting patterns of these strains consistently showed five different genetic clusters. Strains belonging to serovar Ratnapura that caused hepato-renal involvement in patients in South India were genetically dissimilar to strains of the same serovar isolated from patients in Andamans who had pulmonary complications. Strains of other serovars causing mild and sever illness could also be discriminated. However, isolates obtained from human patients and rodents in the same geographical areas showed identical fingerprint patterns indicating that strains circulating in different geographical regions, though belonging to same serovar, are unique to each region.