Deviations from random mating are an important determinant of plant species evolution. Taxonomic complexity and controversy, and the resulting difficulties in assessing conservation priorities, are often associated with 'critical groups' incongruent with the classic Hardy-Weinberg equilibrium mode of population genetic structure. In critical genera such as Epipactis breeding system transitions are hypothesized to be an important mechanism underpinning speciation. We have erected a multi-gene molecular phylogenetic framework for the Neottieae before using molecular markers to investigate the amounts and partitioning of genetic variability in 26 putative species of Epipactis. These species have contrasting floral morphologies, geographical distributions, habitat preferences, and propensities for vegetative spread. All species with floral morphologies consistent with self-pollination were homozygous and uniform at all examined allozyme loci. In contrast, species whose floral morphologies were consistent with allogamy differed considerably in degrees of genetic variability, with this variability typically organized according to Hardy-Weinberg expectations. Thus, the transition to autogamy has an overriding effect on the organisation of intra-specific genetic variation, but other factors determine the comparative amounts of genetic variation in allogamous species. Using a combination of isozymes, inter-SSRs, cpDNA RFLPs, and cpDNA SSRs, we determined whether autogamous taxa represent distinct lineages rather than minor mutational variants. All of the markers we employed suggest that the transition from allogamy to autogamy is highly iterative, generating multiple homozygous and uniform lineages, each distinct and separable by fixed allelic differences from other comparable lineages.

Key words: breeding system, conservation genetics, Epipactis, molecular markers, Orchidaceae, speciation