Corynespora cassiicola is the causal agent of Corynespora Leaf Fall (CLF) disease. CLF is one of the most important fungal diseases of rubber trees in Asia and Africa but disease outbreaks have not been reported in South America. Cassiicolin, a small cysteine-rich glycoprotein secreted by the pathogenic C. cassiicola isolate CCP, was previously identified as a potential disease effector in rubber tree. Recently, the cassiicolin-encoding gene (Cas1) was characterized and shown to be expressed in the early phase of infection. In this study, we investigated whether previously undetected strains of C. cassiicola are present in South American rubber plantations by examining the fungal endophyte population found in asymptomatic rubber tree leaves. Four isolates were identified as C. cassiicola. Genes encoding new forms of the cassiicolin precursor protein (Cas3 and Cas4) were identified from these isolates. Three of four isolates were able to induce symptoms on the cultivar they were isolated from in a detached leaf assay, with different kinetics and intensities. One isolate had the same pathogenicity profile as the pathogenic isolate CCP; the other two isolates developed symptoms late during the course of infection, suggesting saprotrophic capabilities. However, no Cas3 or Cas4 transcripts could be detected upon inoculation with the endophytic isolates, whereas the reference gene Cas1 was expressed upon inoculation with the CCP isolate. This work demonstrated that C. cassiicola is present in South America in an endophytic form and that it may evolve from an endophytic to a saprophytic or even potentially pathogenic life style.