Arachnorchis concolor and A. pilotensis are two rare orchid species with contrasting spatial distributions found in south-eastern Australia. A. concolor is known from ~220 plants, with the largest population found in southern central Victoria and the remaining smaller populations ~100 km north. Some taxonomic uncertainty surrounds the affiliations of these disjunct populations. A. pilotensis is known from ~100 plants in a single location near the Beechworth region of north-eastern Victoria. Small populations such as these can show extreme demographic and/or genetic constraints and careful management is required to ensure their long-term persistence. The present study used amplified fragment length polymorphism (AFLP) markers to describe the levels of relatedness among plants from both species and to determine levels of genetic diversity for each species as well as levels of differentiation among A. concolor populations, to assist with species management. Species-level genetic diversity was lower in A. pilotensis (PLP 44%, Hj 0.182) than A. concolor (PLP 58.2%, Hj 0.202). Genetic diversity also varied among A. concolor populations but this does not appear to relate to population size. High levels of inbreeding were evident in A. concolor (f, 0.828) in contrast to moderate levels observed in A. pilotensis (f, 0.466). Genetic relatedness maps, generated by principal coordinates analyses, indicated significant differentiation among A. concolor populations with some sub-structuring also apparent within A. pilotensis. Management implications for the two species, with respect to sourcing of material for translocation and augmentation of pollination events within populations, are discussed in light of these findings.