Plum pox virus (PPV) severely damages and reduces the yield of stone fruits. Among the nine identified strains (An, C, CR, D, M, EA, Rec, T and W), strain D is widely disseminated, and causes the most outbreaks outside Europe. Recently, PPV-D isolates were detected in different provinces of Turkey. However, no information is available about the whole-genome sequence of PPV-D in Turkey (PPV-DT), which is important to understand the epidemiology of PPV strains. In this study, we have determined the whole-genome sequences of six PPV-D isolates. The nucleotide and amino acid composition of PPV-DT isolates was found to be similar to that of PPV-D isolates deposited in GenBank. Intragroup diversity was found to be slightly higher (1.34%) in six Turkish D isolates than for 13 global D isolates (1.27%). Recombination analysis identified five recombination events involving Turkish D isolates, and a sample called Istanbul8 exhibited two recombination events. Global D and Turkish D isolates differed at 111 amino acid positions. Turkish D isolates were found to be closer to EA, M, Rec and T strains rather than global D isolates at the amino acid sequence level. The findings suggest that PPV-D isolates in Turkey are not a recent introduction to the country.