Knowledge of genetic structure at different scales is necessary for evaluating the importance of interactions between the genome and environment and for inferring underlying processes that bring about evolutionary diversification. Here, genetic and morphological variation was assessed for 154 individuals of Platanthera aquilonis and P. dilatata in Maine, using RAPD and PCR-RFLP markers and measurements of five morphological traits to determine the prevalence of interspecific hybrids and underlying spatial genetic structure of the population. Both species co-mingled in the population, but clumping was observed. Platanthera aquilonis was more abundant, but genetic variation was lower (polymorphic loci [40%], expected heterozygosity [0.137]) than that of P. dilatata (P(p) = 72%; H(e) = 0.245). Interspecific hybrids were rare (eight individuals), and morphology was not consistently reliable for determining hybrid status even though the species differed significantly in several traits. Spatial autocorrelation analyses showed significant genetic structure at small distances for both species, most likely due to restricted seed dispersal. Platanthera aquilonis did not exhibit a pattern of spatial genetic structure consistent with other selfing species. This suggests that the species is facultative autogamous, which allows for limited production of hybrid individuals and reduces the strength of spatial genetic structure relative to P. dilatata.