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During storage and ripening, mango fruit develop stem-end rots (SER) that reduce quality, causing significant losses of harvested fruit. The presented results indicate that pathogens, endophytically colonizing the fruit’s stem end, awaken during fruit ripening and cause SER. The main pathogens causing SER in mango grown in Israel were found to be Alternaria alternata and Lasiodiplodia theobromae. Confocal analysis of the sliced stems indicated that the pathogens endophytically colonize the phloem of the fruit’s stem end; they branch into the fruit parenchyma when the pathogen switches to its actively pathogenic stage. We show that the stem ends are also colonized by other microorganisms, including fungi, yeast, and bacteria, which do not cause any apparent symptoms and are considered as true endophytes. Stem-end microbiomes of red (resistant) compared with green (susceptible) mango stored at optimal …