Thaumetopoea pityocampa, the winter pine processionary moth, is one of the most important pests of pine trees in the Mediterranean region. To learn more about the refugial areas within the greater refugium of Greece, samples from 15 local populations were collected. Analysis of the Cytochrome Oxidase I region identified 15 haplotypes. One strongly supported clade was found, separating the Aegean island of Lesvos from the mainland populations. Mdiv analysis showed that this clade diverged from the general clade 155,000 y.a., suggesting the sea level changes during the Quaternary Period as a possible reason for its seclusion. Additionally, comparisons with similar studies in this region revealed a possible colonization of the eastern Aegean islands from the Turkish mainland rather than from Greece. However, no strong isolation-by-distance events were detected among the mainland populations, which could be attributed to the joint effect of regular gene flow and the lack of insurmountable geographic barriers. Finally, regarding population structure, Bayesian analysis as well as neutrality tests pointed towards an ongoing population expansion which verifies the potential invasiveness of this pest species, something that will have to be dealt with under the influence of climate change.