The seed mycoflora associated naturally with oil seeds causes seed deterioration making them unfit for consumption and oil extract. The seed borne fungi inhibits seed germination, seedling emergence and causing diseases to crop plants. The major factor affecting the spoilage of stored oil seeds by moulds, moisture content and temperature. The seed mycoflora of oil seeds like soybean (JS-335, Prasad and Puja), Safflower (Tara, Bhima and Sharda) and Niger (Local, N-8 and Ootcamand) was detected by standard blotter method and agar method. The most dominant fungi detected on three varieties of soybean were Rhizopus stolonifer, Curvularia lunata, Aspergillus niger, Alternaria alternata, from Safflower Alternaria tenuis, Aspergillus niger, Rhizopus stolonifer and from Niger Alternaria tenuis, Aspergillus niger, Rhizopus nigricans. It was found that temperature invariably affect the quality of the seeds in the storage. The percentage incidence of fungi found varies at different temperatures. The temperature 30°C was found to be more favorable for the incidence of fungi on oil seeds. A very less percentage incidence of fungi was found at 10°C and 40°C temperature tested for all the varieties of Soybean, Safflower and Niger.