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Genomic DNA isolated from embryogenic cultures of two mango cultivars, ‘Hindi' and ‘Carabao,' that had been selected for resistance to the culture filtrate of Colletotrichum gloeosporioides, was analyzed using Randomly Amplified Polymorphic DNA (RAPD). In vitro selection caused changes in RAPD markers in the selected embryogenic cultures with respect to the unchallenged control cultures and the stock plants. The differences involved both the absence and the presence of additional RAPD markers in the resistant lines, although the former was most commonly observed. The absence of differences between the unchallenged control of either cultivar and DNA from the leaves of parent trees confirmed that the changes were not due to prolonged maintenance in liquid cultures.