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Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in <i>Arabidopsis</i> associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 <i>Arabidopsis</i> accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, <i>At1g63005</i> (<i>miR399b</i>) and <i>At2g05635</i> (<i>DEAD helicase RAD3</i>), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.