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The genetic diversity and evolutionary history of the epidemic plum pox virus strain M (PPV‐M) have been poorly studied. We sequenced the genomes of 69 PPV‐M isolates selected from different Turkish regions. These new nearly full‐length genomic sequences were analysed together with 21 previously reported Turkish sequences of the PPV‐MIs clade and with 50 sequences of other PPV‐M isolates collected worldwide, including four sequences of Albanian isolates. Major genomic features were maintained in all new PPV‐M genomic sequences, with the highest divergence detected in the PIPO, P1 and CP proteins. Turkish PPV‐M isolates displayed a high genetic diversity and grouped into two sister clades, one formed by PPV‐MIs isolates only and a second clade consisting of the previously described PPV‐Ma and PPV‐Mb subclades. The combined diversity for PPV‐M isolates (Europe, Japan and Turkey) reached to 0.022 ± 0.001, which is slightly higher than the diversity of the globally distributed PPV‐D strain (0.017 ± 0.001). Likewise, the genetic diversity of PPV‐M (0.020 ± 0.001) in Turkey was found to be comparable to that observed for PPV‐M isolates from other countries (0.021 ± 0.001) and even marginally higher if considering partial genomic sequences that allow the inclusion of a much larger number of isolates and countries. Overall, the original distribution of PPV‐MIs, which seems to be almost specific to Turkey, and the high genetic diversity of PPV‐MIs and other Turkish PPV‐M isolates suggest a long evolutionary history of M isolates in Turkey and position this country as a centre of diversity of PPV‐M. [ABSTRACT FROM AUTHOR]