Chlorpyrifos is one of the broad-spectrum organophosphate insecticides in controlling plant pests. They can be absorbed into agricultural products and in the long term can have negative effects on human health. The use of endophytic fungi for biodegradation of chlorpyrifos is one of the technologies to support food safety. Therefore, this study was aimed to determine the potential of the isolated endophytic fungi and identify it from shallot plantations as biodegradation of chlorpyrifos. The research is conducted in three stages; (1) isolation of endophytic fungi on shallot plantations in Bantaeng Regency, (2) macroscopic and microscopic identification, and (3) test of the degradation potential of chlorpyrifos by growing fungi on PDA medium containing chlorpyrifos with concentrations 600 ppm, 300 ppm, and 150 ppm. Furthermore, the results showed there are 47 fungal isolates from the roots, stems and tubers of shallots, and some were identified as Trichoderma sp. and Fusarium sp. Several isolates tested have the potential to degrade chlorpyrifos, where the percentage of growth inhibition below 50% is considered tolerant of chlorpyrifos. Considering the results, Trichoderma sp. and Fusarium sp. are potential degrading residual insecticide chlorpyrifos.