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Leaf ecophysiological traits related to carbon gain and resource use are expected to be under strong selection in desert annuals. We used comparative and phenotypic selection approaches to investigate the importance of leaf ecophysiological traits for Helianthus anomalus, a diploid annual sunflower species of hybrid origin that is endemic to active desert dunes. Comparisons were made within and among five genotypic classes: H. anomalus, its ancestral parent species (H. annuus and H. petiolaris), and two backcrossed populations of the parental species (designated BC2ann and BC2pet) representing putative ancestors of H. anomalus. Seedlings were transplanted into H. anomalus habitat at Little Sahara Dunes, Utah, and followed through a summer growing season for leaf ecophysiological traits, phenology, and fitness estimated as vegetative biomass. Helianthus anomalus had a unique combination of traits when compared to its ancestral parent species, suggesting that lower leaf nitrogen and greater leaf succulence might be adaptive. However, selection on leaf traits in H. anomalus favored larger leaf area and greater nitrogen, which was not consistent with the extreme traits of H. anomalus relative to its ancestral parents. Also contrary to expectation, current selection on the leaf traits in the backcross populations was not consistently similar to, or resulting in evolution toward, the current H. anomalus phenotype. Only the selection for greater leaf succulence in BC2ann and greater water-use efficiency in BC2pet would result in evolution toward the current H. anomalus phenotype. It was surprising that the action of phenotypic selection depended greatly on the genotypic class for these closely related sunflower hybrids grown in a common environment. We speculate that this may be due to either phenotypic correlations between measured and unmeasured but functionally related traits or due to the three genotypic classes experiencing the environment differently as a result of their differing morphology.