In this study we investigate the use of 2D and 3D scanning optical coherence tomography (OCT) technology for use in apple blotch diagnosis. In order to test the possible application of OCT as a detection tool for apple trees affected by Marssonina coronaria, we conducted several experiments and compared the results from both healthy and infected leaves. Using OCT, we found several distinctive features in the subsurface boundary regions of both the diseased and healthy leaves. Our results indicate that leaves from diseased trees, while still appearing healthy, can be affected by M. coronaria. The A-scan analysis method confirmed that the boundaries found under the subsurface layers can be faint. This shows that M. coronaria can exert its influence on entire apple trees (as opposed to only on leaves with lesions) once it infects healthy trees. Our results indicate that OCT can be used as a noninvasive tool for the diagnosis of fungal disease in apple trees. Microscopic imaging results, performed as a histological study for comparison, correlated well with the OCT results.