Prunus necrotic ring spot ilarvirus (PNRSV) and Apple chlorotic leaf spot trichovirus (ACLSV) are common in plum orchards. The aim of the study was to obtain virus-free planting material of Prunus domestica L. by chemotherapy in vitro. Ribavirin at concentrations of 10 to 50 mg·l−1 was added to Murashige–Skoog (MS) nutrition medium for virus eradication from microshoots. After a two-week period of chemotherapy, meristems were subcultured monthly on MS medium and proliferation index of shoots was estimated. Microshoots were retested by reverse transcription polymerase chain reaction for presence of virus. At lowest concentrations of 10 mg·l−1 ribavirin was entirely ineffective for ACLSV and 10 to 30 mg·l−1 was ineffective for PNRSV elimination. Ribavirin concentrations of 40 and 50 mg·l−1 destroyed both pathogens. However, at higher concentrations of 40 and 50 mg·l−1 ribavirin exhibited some signs of phytotoxicity on microshoots in the first sub-cultivation period. In order to test the genetic stability of the microplants after chemotherapy the amplified fragment length polymorphism (AFLP) method was applied. Plant genome stability in ‘Magna Glauca’ at concentrations of 40 mg·l−1 was damaged, as the presence of polymorphic AFLP markers were observed.