The genetic variation of wild blueberries species has been the focus of considerable interest around the world, especially in relation to their commercial potential. Vaccinium myrtillus is a native European berry commonly found throughout central and north Europe. Little is currently known about the genetic variation of European wild blueberries and its relation to their geographic distribution. Here we analysed the genetic diversity of Scottish wild blueberries by means of SSRs markers, and found significant genetic flow throughout the region, not directly correlated with the geographic distances among locations. Our results highlight a higher genetic diversity of blueberries growing in grasslands rather than woodlands, hinting to local adaptation. Future studies involving a more extended sampling are highly recommended to explore the current genetic variation of Scottish blueberries and their potential for commercial exploitation.