The distribution of Plum pox virus (PPV), Prune dwarf virus (PDV), Prunus necrotic ringspot virus (PNRSV), Apple chlorotic ringspot virus (ACLSV) and Apple mosaic virus (ApMV) in naturally growing shrubs of blackthorn and road-bordering trees of plum and myrobalan, and of PPV, PDV, PNRSV and Cherry leafroll virus (CLRV) in sweet and sour cherry trees were investigated. The most widely distributed viruses were PPV in plums (74% of the investigated trees were infected); PPV, PDV, and PNRSV in myrobalans (26%, 11% and 18%, respectively), PDV in blackthorns (27%), and PDV and PNRSV in cherries (25% and 22%). PPV was not detected in sweet and sour cherries. The incidence of ACLSV and ApMV was negligible in individually growing trees of the genus Prunus in the Czech Republic.