Jatropha curcas (L.) commonly called purging nut or physic nut is a multi-purpose drought resistant shrub or small tree belonging to the family Euphorbiaceae. The plant is gaining a huge attention lately because of the great economic importance associated with it. Jatropha curcas is susceptible to attack by microorganisms and the correct identification of these microbes is necessary for the development of sustainable disease prevention/control measures. This study was aimed at isolating and characterizing fungi associated with the leaves of J. curcas collected from Aluu in Rivers State, Nigeria. Fungi were isolated using microbiological conventional culturing method and identified using molecular method. Genomic DNA was extracted from fungal isolates using Zymo Fungal/Bacterial DNA Miniprep Kit. Polymerase chain reaction amplification was carried out using the primer pair: ITS4 and ITS5. BLAST search was carried out on National Centre for Biotechnology Information (NCBI) database and the species identity of the two fungal organisms associated with Jatropha curcas revealed that the organisms are two different strains of Colletotrichum siamense. Phylogenetic tree revealed the relationship among the two strains, other strains/isolates of Colletotrichum siamense and other species of Colletotrichum on GenBank. The sequences of the isolates have been deposited in GenBank under the accession numbers: OQ941591 for Colletotrichum siamensestrain RCBBR_AEANK17 and OQ941592 for Colletotrichum siamensestrain RCBBR_AEANK18. The basic molecular techniques used in this study were able to classify the isolates to the species and strain levels.