There has been a long-standing debate as to whether Sympetrum striolatum (Charpentier, 1840) and the darker northern form, S. nigrescens (Lucas, 1912) should be recognised as separate species of dragonfly. Here we address this question using genetic analysis based on AFLP markers and samples collected from sites across the species' United Kingdom range. The program STRUCTURE finds no support for specific status. Instead, it reveals strong patterns of divergence between populations sampled from Scottish islands and those on the mainland, suggesting that salt water is a major barrier to gene flow. Thus, the dark form is quite likely to reflect a beneficial polymorphism that allows individuals to take advantage of short periods of warmer weather. Our AFLP markers appear to be very rapidly evolving, showing little or no overlap between congeneric species, and hence are ideally suited to answering questions relating to the levels of gene flow among populations within species.