Diploid hybrid speciation in plants is often accompanied by rapid ecological divergence between incipient neospecies and their parental taxa. One plausible means by which novel adaptation in hybrid lineages may arise is transgressive segregation, that is, the generation of extreme phenotypes that exceed those of the parental lines. Early generation (BC₂) hybrids between two wild, annual sunflowers, Helianthus annuus and Helianthus petiolaris, were used to study directional selection on transgressive characters associated with the origin of Helianthus paradoxus, a diploid hybrid species adapted to extremely saline marshes. The BC₂ plants descended from a single F₁ hybrid backcrossed toward H. petiolaris. The strength of selection on candidate adaptive traits in the interspecific BC₂ was measured in natural H. paradoxus salt marsh habitat. Positive directional selection was detected for leaf succulence and Ca uptake, two traits that are known to be important in salt stress response in plants. Strong negative directional selection operated on uptake of Na and correlated elements. A significant decrease in trait correlations over time was observed in the BC₂ population for Na and Ca content, suggesting an adaptive role for increased Ca uptake coupled with increased net exclusion of Na from leaves. Patterns of directional selection in BC₂ hybrids were concordant with character expression in the natural hybrid species, H. paradoxus, transplanted into the wild. Moreover, the necessary variation for generating the H. paradoxus phenotype existed only in the BC₂ population, but not in samples of the two parental species, H. annuus and H. petiolaris. These results are consistent with the hypothesis that transgressive segregation of elemental uptake and leaf succulence contributed to the origin of salt adaptation in the diploid hybrid species H. paradoxus.