A combination of allozyme and mitochondrial DNAmarkers were used to determine the contributionof recent and ancient causes of patterns ofgenetic variation within and among 46populations of the endangered golden sun moth,Synemon plana. Allozyme analysis groupedthe 46 populations into 5 major geneticclusters that corresponded closely withgeographic location following a classicisolation-by-distance model. Phylogeneticanalysis of 14 mtDNA haplotypes revealed tworeciprocally monophyletic groups. One of thesegroups (containing 4 geographically distantpopulations) was clearly identified by allozymeanalysis and represents a distinct evolutionaryunit. The remaining 4 allozyme groups were notdistinguishable by mtDNA analysis. The evidencesuggests that the populations within thesegroups derived from a small founding populationthat underwent rapid demographic expansion inancient times. This was followed by more recentpopulation bottlenecks resulting from habitatfragmentation associated with the widespreadintroduction of agriculture into the region.The generally low levels of allozyme andnucleotide diversity within these populationssupport this hypothesis.