Most genetic studies on the effects of water and salt stresses on seed germination have used conditions that are more extreme than those found in nature. Vallejo et al. apply relatively mild stresses to seeds of Arabidopsis thaliana accessions and find two loci associated with the salt sensitivity response and four associated with the osmotic sensitivity response, one of which only appears to act under mild stress. The regulation of germination under moderate salt and osmotic stresses involves the action of independent major loci, revealing the existence of loci specifically associated with the toxic component of salt and not just its osmotic effect.