A single gene with pleiotropic effects accounts for the Scottish endemic taxon Athyrium distentifolium var. flexile.

•  Experiments were conducted to determine the genetic relationship between the alpine fern Athyrium distentifolium and the Scottish endemic taxon A. distentifolium var. flexile. •  Segregation of the taxa was studied after growing sporophytes from spore families, and after selfing and crossing gametophytes. The growth of both gametophytes and sporophytes was measured under a range of nutrient regimes. •  The distinction between the two taxa is due to variation at a single gene with pleiotropic effects expressed at both the sporophyte and gametophyte stages. A. distentifolium sporophytes (genotypes A /A or A /A ) are taller, have fewer fronds, and produce fewer spores than A. distentifolium var. flexile sporophytes (genotype A /A ). Gametophytes containing the A allele have a 50% higher growth rate than those with the A allele on a range of media. •  The polymorphism may be maintained by a balance between selection for and against the A allele at the gametophyte and sporophyte stages of the life cycle, respectively. Implications for the conservation of the A. distentifolium var. flexile taxon are discussed.