Abstract Prune dwarf virus (PDV) is a member of the Ilarvirus genus which is widely spread all over the world and causes considerable economic losses in nurseries and orchards. The virus is transmitted via seeds and pollen and through vegetative reproduction. However, the mechanisms of cell-to-cell and systemic transport of the virus are still not known. For the first time this study presents phylogenetic characterization of the movement protein (MP) of PDV isolates from the GenBank database in the context of geographic origin. The prepared analyses were based on a comparison of the whole amino acid sequence of the MP-PDV, the RNA-binding domain (RBD) in MP of PDV and MPs of four viruses from the Bromoviridae family with known transport mechanisms. Two different bioinformatic programs ClustalW and Jalview were used, and MP sequence variability up to 8% at the amino acid level among PDV isolates was confirmed. In the constructed phylogenetic trees the isolate sequences clustered in three conserved groups. Further analyses revealed similarity of the MP amino acid sequence of PDV and Alfalfa mosaic virus (AMV) of up to 34% and a 40% similarity of RBD between these viruses which suggested that the PDV transport mechanism may be on some level the same as that for AMV.