Allozyme electrophoresis was used to assess levels of genetic variation and diversity and investigate patterns of population structure in the endangered golden sun moth, Synemon plana. Twenty populations were sampled from throughout the geographic range of the species. Levels of genetic variation within most populations were lower than that observed in other lepidopteran species. The evidence suggests that this level of variation may have resulted from population bottlenecks and founder events following habitat fragmentation. Five distinct groups of S. plana populations have been identified which correspond closely with geographic location. One of these groups may be sufficiently different genetically to be regarded as a separate subspecies or race. These five groupings should be treated as separate units for conservation management.