Fungal decay is one of the most common diseases that affect postharvest operations and sales of citrus. Sometimes, fungal disease develops and spreads inside the fruit and in the advanced stages of the disease, it appears apparent, so the use of efficient and reliable methods for early detection of the disease is very important. In this study, early detection of citrus black rot disease caused by Alternaria genus fungus was examined using spectroscopy. Jaffa oranges were inoculated with Alternaria alternata. The samples were inspected by spectroscopy (200–1100 nm) in the 1st, 2nd, and 3rd weeks after inoculation. The classification of healthy and infected samples and selection of most important wavelengths were conducted by soft independent modeling of class analogy (SIMCA). The most important wavelengths in the detection of healthy and infected samples of the 1st week were 507, 933, 937, and 950 nm with a classification accuracy of 60%. The most important wavelengths of the 2nd week were 522 and 787 nm with a classification accuracy of 60%. Also, wavelengths of 546, 660, 691, and 839 were found to be effective in the 3rd week with a classification accuracy of 100%.

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