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Salt tolerance varies between species and genotypes of plants, but evaluation of these differences is cumbersome, because whole plants that are highly complex systems show a variety of responses depending on the applied methodology. However, focusing on plant roots, which are in direct contact with the soil, could offer a simpler and more efficient model for analyzing salt stress tolerance in different species. This study explores whether root growth under salt stress is associated with genotypic differences in Prunus species with different degrees of salt tolerance. Excised root cultures were grown in vitro under increasing salt concentrations (0, 20, 60, and 180 mm NaCl). Root tips taken from in vitro-rooted shoots of Prunus species with different salt tolerance were measured after 3 weeks of culture in a shaker, and changes in their anatomy were examined. Both growth and starch content of in vitro root cultures were affected by salt concentration. Root length increments were related to salt stress tolerance at 60 mm NaCl, in which significant differences were also found between species. A significant inverse correlation was found between salt tolerance and starch accumulation in the maturation zone of root tips. Genotypic differences were observed in agreement with species' salt stress tolerance in vivo. These results suggest the use of excised root cultures for rapid, early detection of salt stress tolerance in plants. Chemical names: sodium chloride (NaCl).