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The ascomycete fungus <i>Venturia inaequalis</i> causes scab disease, a major problem in apple production. The utilization of resistant cultivars is hindered by emerging new pathogen races, which erode their resistance. Increasing our knowledge on the population genetic processes of the fungus can contribute to the development of resistance gene deployment strategies and more durable resistance. We investigated the effect of four scab race indicator cultivars, ‘Gala’ (no <i>R</i>-gene), ‘Golden Delicious’ (<i>Rvi1</i>), ‘Geneva’ (<i>Rvi3</i>, complex), and OR45t132 (<i>Rvi5</i>), on the <i>V. inaequalis</i> population genetic structure and diversity. Sixty-six monosporic fungal isolates from the four cultivars were genotyped with seven simple sequence repeat primers. Furthermore, the partial resistance of the indicators and the pathogenicity profile of the conidia from each host were assessed. The genetic diversity and structure of the investigated <i>V. inaequalis</i> subpopulations correspond to the partial resistance of the original hosts as well as the subpopulations’ pathogenicity profiles. Indicators carrying <i>Rvi3</i> and <i>Rvi5</i> had strongly diverged and specialized <i>V. inaequalis</i> populations on them and fewer symptoms on the field. In line with the complete breakdown of the <i>Rvi1</i> gene, the population from ‘Golden Delicious’ did not segregate from the susceptible ‘Gala’, and virulence towards <i>Rvi1</i> was present in all subpopulations.