There is increasing evidence that short tandem repeats (STRs) -mutational hotspots present in genes and in intergenic regions throughout most genomes -may influence gene and protein function and consequently affect the phenotype of an organism. However, the overall importance of STRs and their standing genetic variation within a population, e.g. if and how they facilitate evolutionary change and local adaptation, is still debated. Through genome-wide characterization of STRs in over a thousand wild Arabidopsis thaliana accessions we demonstrate that STRs display significant variation in length across the species' geographical distribution. We find that length variants are correlated with environmental conditions, key adaptive phenotypic traits as well as gene expression levels. Further, we show that coding STRs are overrepresented in putative protein interaction sites. Taken together, our results suggest that these hypervariable loci play a major role in facilitating adaptation in plants, and due to the ubiquitous presence of STRs throughout the tree of life, similar roles in other organisms are likely.