Corynespora cassiicola is an anamorphic pathogenic fungus belonging to the phylum Ascomycota with a broad host range. It causes the Corynespora leaf fall (CLF) disease, in rubber trees for which it badly affects natural rubber production. A small phytotoxic protein named cassiicolin derived from the cassiicolin gene (Cas gene) of the fungus was thought to be inducing the pathogenicity in rubber tree; however, some of the isolates that do not possess cassiicolin gene shows aggressiveness on the host. The present study intends to identify the effect of cassiicolin and other putative effectors involved in CLF disease. Comparative screening of the crude toxin extracted from 30 isolates was carried out for cassiicolin activity and the Cas isoform was determined. The isolate named HV showed maximum aggressiveness and the presence of a Cas gene isoform (Cas2). It was sequenced, assembled, and confirmed for the presence of Cas2 isoform of the Cassiicolin gene. This is the first report of an Indian isolate having a Cas-2 isoform from Hevea brasiliensis. The phylogenetic analysis reveals the similarity of Cas gene from HV to Cas2 gene of CC004 strain of China. The effector proteins present in the isolate (HV) were identified. A total of 1035 effector proteins were predicted, among them 1026 were matched with the DFVF database, and in which 229 are classified as leaf spot-associated virulence factors. The predicted gene and proteins were mostly associated with carbohydrate and amino acid metabolism. Identification of specific effectors involved in the pathogenicity helps to step towards the understanding of C. cassiicola virulence and host–pathogen interaction. The data of this work and its future aspects will furnish the facts behind the interaction between the Hevea and Corynespora.