The aim of the present study was to check the deterioration of Jatropha curcas L. seeds during storage. Agar plate and standard blotter methods were used to study the seed-borne mycoflora of Jatropha curcas L. Both surface sterilized and unsterilized seeds were taken for isolation of fungi. Surface sterilization was done by 0.1% mercuric chloride (HgCl2) solution. A significant contamination with fungal genera was detected in analyzed stored seeds. Sixteen fungal species with two strains of Aspergillus flavus i.e., brown and green were isolated from physic nut seeds during one year of storage. Fungi isolated and identified were Alternaria alternata, Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Aspergillus terreus, Cephaliophora irregularis, Chaetomium globosum, Cladosporium cladosporioides, Curvularia lunata, Fusarium moniliforme, Fusarium roseum, Penicillium citrinum, Penicillium rubrum, Rhizopus stolonifer, Dark sterile mycelium and White sterile mycelium. This is the first report of Cephaliophora irregularis on Jatropha curcas L. seeds. Agar plate method showed better results for isolation of Chaetomium globosum, Cladosporium cladosporioides, Curvularia lunata and Fusarium moniliforme.