The facultatively halophytic Lophopyrum elongatum, closely related wheat, Triticum aestivum, and their amphiploid tolerate salt stress better if they are gradually exposed to it than if they are suddenly stressed. Lophopyrum elongatum has greater tolerance of both forms of salt stress than wheat, and its genome partially confers this tolerance on their amphiploid. Chromosomal control of the tolerance of both stress regimes in the L. elongatum and wheat genomes was investigated with disomic and ditelosomic addition lines and disomic substitution lines of L. elongatum chromosomes in wheat and with wheat tetrasomics. The tolerance of the sudden salt stress is principally controlled by L. elongatum chromosomes 3E and 5E and less by 1E, 2E, 6E, and 7E and the tolerance of gradually imposed salt stress principally by chromosomes 3E, 4E, and 5E, and less by chromosome 1E and 7E. Ditelosomic analysis indicated that genes conferring the tolerance of sudden stress are on chromosome arms 1EL, 5ES, 5EL, 6EL, 7ES and 7EL and those controlling the gradual stress regime are on 1ES, 1EL, 5ES, 5EL, 6ES, 7ES, and 7EL. In wheat, chromosomes in homoeologous groups 1, 3, and 7 and chromosomes in homoeologous groups 1, 4, and 6 were shown to enhance the tolerance of suddenly and gradually imposed stress, respectively. The arms of chromosome 3E individually conferred tolerance to neither stress regime. Chromosome 2E and wheat chromosomes 2B and 2D reduce the tolerance of both stress regimes in a hyperploid state. In 2E this effect was associated with arm 2EL. A potential relationship between the tolerance of these stress regimes and the expression of the early-salt induced genes is examined.