Plum pox virus strain M (PPV-M) isolates were previously detected in different districts of Turkey, and they grouped together with European M isolates in phylogenetic trees. However, PPV-M isolates from Istanbul formed a separate group adjacent to European PPV-M isolates. Here, we have obtained full genomes of 10 PPVM isolates from Istanbul derived from apricot and peach trees. The Recombination Detection Program version 4.16 (RDP4) was used for recombination analysis of 51 genomes of PPV, including the 10 full genomes of PPV-M Istanbul and six Turkish PPV-D isolates. Genome sequences were selected from GenBank to represent global PPV variation. Recombination events, likely parental isolates of recombinants and recombination break points were analysed using nine independent recombination detection methods (RDP, Bootscan, Geneconv, Maxchi, Chimaera, Siscan, 3seq, Lard and Phlopro) implemented in the RDP4 program with default settings. The program identified 19 recombination events. Of the total events, 13 recombination events included Turkish PPV-M and PPV-D isolates. Seven of the recombination detection methods showed that isolates from the PPV-Rec strain (AF357541, GU461889, EU117116, GU474956 and JX013532) included in the 51 genomes are likely to contain recombinant fragments from the one of the Turkish PPV-D isolates and a PPV-M isolate from Istanbul. Recombination events among the 10 PPV-M isolates were also detected at the intrastrain level. This is possible because all PPV-M Istanbul isolates were collected from a narrow district in Istanbul. Genome nucleotide comparisons revealed that PPV-M isolates from Istanbul had identity with European PPV-M, PPV-T, PPV-An, PPV-Rec, PPV-D, PPV-EA, PPV-CR, PPV-W and PPV-C of 97, 94, 92, 89, 88, 076, 74, 74 and 73%, respectively. The average intragroup diversity was found to be 0.014 for the Turkish PPV-M group (10 isolates) and 0.019 for the European PPV-M isolates (four isolates).