Hemileuca maia (Bog Buckmoth; Saturniidae) is a rare, ecologically unique variant of the Hemileuca maia complex known only from ten wetlands in the Great Lakes region of North America. The Bog Buckmoth's status as a threatened taxon meriting conservation has been subject to a debate largely centered on its degree of evolutionary isolation and species status. We studied the genetic variation of two New York Bog Buckmoth populations using amplified fragment-length polymorphisms (AFLP). Bayesian clustering analysis identified two genetically distinct population clusters, with membership that did not coincide consistently with the two sampled populations. There appears to be either historical or contemporary gene flow between Bog Buckmoth populations, with the results suggesting either dispersal between the two sampled populations or contributions from a third unsampled population. Genetic diversity levels were similar. These findings argue for the utility of population-level analyses of Bog Buckmoth as a tool in conservation practice as well as in understanding the taxon's evolutionary history.