Monilinia linhartiana is a significant fungal pathogen of quince causing leaf blotch, shoot blight and mummification of developing young fruits. In our study, five isolates originating from infected quince shoots were characterized. Morphological characteristics were determined before performing molecular assays. Three genomic regions were sequenced and analysed: the ITS region, a polymorphic region and the β-tubulin gene. The ITS region (ITS1-5.8 rDNA-ITS2) sequences of different Monilinia species showed high similarity, thus M. linhartiana isolates could not be safely separated from M. aucupariae isolates. By converse, based on the 28S rDNA sequences, M. linhartiana isolates could be distinguished from the closely related species, offering prospects for the unambiguous identification of Monilinia species. The 28S rDNA and β-tubulin genes of M. linhartiana were sequenced for the first time.