Plants dynamically cope with the variability of mineral nutrient distribution in soil by constantly modulating nutrient uptake and shaping root-system architecture. The changes in root morphology in response to major essential elements are largely documented, but little is known about how the root system responds to magnesium (Mg) availability. Thirty-six natural accessions of the model species Arabidopsis thaliana were subjected to an in vitro screen for identifying variation in root system architecture in response to Mg availability. Response of root morphology was observed on 2-dimensional agar plates. Low Mg supply repressed the elongation of the lateral roots more than of the primary root. However, some accessions exhibited higher number and length of lateral roots than the reference Columbia-0. Across all accessions, the root morphological traits did not correlate with tissue Mg concentrations. Interestingly, shoot calcium and root phosphorus concentrations were positively correlated with the number and length of lateral roots, whereas root iron concentration was negatively correlated with the primary root length. The diversity of root phenotypes identified in this report is a useful resource to study the genetic component determining root morphology in response to Mg availability.