<p>Potato virus Y (PVY) has been reported as one of the pathogens hampering production of potato (<i>Solanum tuberosum</i> L.) in Türkiye, but the genetic diversity of Turkish isolates is still largely unknown. Four hundred and forty-seven samples from Afyon, Bolu, Nevşehir, and Tokat Provinces in the central region of Türkiye, where most of the country’s cultivation is performed, were molecularly tested for PVY in this study. Sequences of partial P1, complete HC-Pro, and complete P3 gene regions (concatenated length of 3258&#xa0;nt) were obtained for 25 of 197 (44.07%) positive tested isolates, randomly selected to represent each province. Twenty-two Turkish isolates were positioned in N group while three other Turkish isolates, including two recombinant isolates (S9-10 and Sa12-8), were included in NTN group in the constructed phylogenetic tree. Members of the recombinant NTN group were shown to have high diversity among them according to population analysis using DnaSP software. However, negative values given by neutrality tests demonstrated that the NTN group is undergoing balancing selection. The consistently large fixation index values (<i>F</i>_ST &gt; 0.33) calculated for comparisons between different groups confirmed their distinction from each other. This research contributed to our understanding of the genome variations among Turkish isolates and the evolution of PVY.</p>