In the past several years, a limited number of isolates of a diverse group of Plum pox virus (PPV) strain -M were discovered in the European part of Istanbul, Turkey. In this study, stone fruit samples were collected from the European part of Istanbul and investigated by PCR typing and sequence analyses for determining prevalence and genetic diversity of this divergent PPV-M isolates. Out of the 230 sampled trees, 97 were determined to be infected with PPV. Strains of 88 isolates were identified and 67 of them (76%) were divergent PPV-M isolates, detected in apricot, peach and plum trees revealing that they could be evolutionarily successful divergent PPV-M isolates prevalent in Istanbul. The divergent Istanbul M isolates formed a monophyletic clade thereby named as PPV-MIs. Additionally, recombination analysis suggested that PPV-MIs isolates could be the donor of the PPV-M-type recombinant fragment of the PPV-Rec strain.