This dataset shows how the genotypic data stored in "Genotypic data at microsatellite loci of Abies alba (Mill.) in the Pyrenees" (https://doi.org/10.15454/HVPAON) was analyzed. The dataset contains which genetic diversity and clustering, demographic inference and ecological correlation methods and information that were used to produce the results presented in a paper published in Ecology and Evolution, called: Signature of mid-Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin (DOI: 10.1002/ece3.7886). This data set is composed of files that are supplementary material to the paper.