The dataset contains genotypes for samples used to validate a 50K single nucleotide polymorphism (SNP, DNA mutation) Axiom array for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex. Full details about this dataset can be found at https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2