Identification of fungal races/pathotypes by using morphological criteria alone is difficult. Hence, molecualr markers were used in the present study to characterize the pathogen causing leaf diseases of rubber. Molecular characterization of the Colletotrichum isolates showed two major RAPD profiles suggesting the possibility of involvement of two different fungi inciting different disease symptoms, raised spots, Anthracnose and circular papery lesions of Hevea. RFLP analysis of ribosomal DNA spacers (ITS 4/5) including 5.8S ribosomal DNA also reflected two groupings of the Collectotrichum isolates confirming the existance of two different Colletotrichum species infecting Hevea. Nucleotide sequence analysis of the r DNAs revealed that the two groups of pathogens belong to two different species of Colletotrichum, namely, C. acutatum and C. gloeosporioides. Genetic structuring of the Corynespora populations, another fungal pathogen of rubber, was carried out through RAPDs. Ten different genotypes/races of Corynespora cassiicola were identified from different rubber plantations in Kerala and Karnataka states. Wide genetic variability was noticed among the Corynespora isolates from Kerala. Knowledge about the existance of different Corynespora races would be very useful to trace the development of new virulent races among the populations for avoiding out breaks of the disease.