Molecular markers have shown a high level of genetic diversity in most extant populations of the federally endangered Lindera melissifolia (Walt.) Blume in the southeastern United States. However, it is unknown if diversity in adaptive traits exists. We quantified adaptive trait variation in 17 L. melissifolia genotypes by growing genets from two disjunct populations in the Lower Mississippi Alluvial Valley in a common-garden environment. We then examined genotype-environment interaction through introduction of a flooding treatment. Within a common-garden environment, variation in adaptive traits was affected by genotype. Stem height, stem diameter, leaf number, and stem architecture accounted for 56% of variation among genotypes, and an additional 23% of variation was attributed to differences in vegetative fecundity and foliar chlorophyll content. There was no divergence in plant morphology between disjunct populations. Plastic response to a winter flooding regime varied in magnitude and direction among male genotypes, and only in magnitude in female genotypes. A decrease in L. melissifolia population sizes would diminish genetic diversity, as well as adaptive trait variation, and may threaten long-term persistence of extant populations.