A Monilinia fructigena-like isolate (UFT) was collected from apple shoots in northeastern Hungary (Újfehértó). Brownish dieback and buff-coloured stromata were observed on shoots and small fruits of cv. ‘Ashton Bitter’. On potato dextrose agar (PDA) the colonies were yellowish in colour and irregular black stromatal crusts occurred. Conidia (16.6 × 10.1 µm) were slightly smaller than the average of M. fructigena. The fungus caused brown rot on inoculated apple fruits, and produced numerous sporodochia. The sequences of the rDNA internal transcribed spacer regions of the UFT isolate were almost identical to that of a previously described Monilia polystroma isolate, containing all five nucleotides that distinguish it from M. fructigena. Comparison of a genomic sequence of unknown function revealed that repetitive sequence motifs occurred in different numbers as insertions in the genomes of M. fructigena, Monilia polystroma, and the UFT isolate. Classical and molecular characterisation indicated that the UFT isolate belonged to Monilia polystroma. To our knowledge this is the first report of Monilia polystroma in Europe.