Molecular variability of PPV isolates was studied using RT-PCR targeting 3'terminal pari of CP gene and RFLP analysis of PCR products. The subgroup differentiation based on RsaI polymorphism of 44 isolates from naturally infected plum, myrobalan, apricot, almond and peach trees revealed the presence of isolates belonging to PPV-M and PPV-D subgroups. PPV-M and PPV-D isolates were almost equally represented in tested samples. Recent studies have discovered the presence of recombinant isolates in Slovakia using a molecular tool based on PPV-M and D subgroup typing targeting P3-6k1, CI and CP regions of the PPV genome. Nearly all the PPV recombinants were recovered from plums and myrobalans; on the contrary, no recombinant was found on peach. The presence of atypical populations of recombinant PPV must be taken into account considering their viability in competition with conventional PPV-M and D isolates.