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The early spring folivore green oak leaf roller moth, Tortrix viridana, is one of the most harmful pests of Palaearctic oaks. The young larvae develop inside flushing buds and therefore require moth egg-hatching and budburst of their host plant to be synchronized. The aim of this study was to understand which factors (geographical distances, oak species, oak leaf phenology and timing of moth egg-hatching) influence the genetic structure of the moth. We performed multilocus analyses (COI and COII mitochondrial genes and eight nuclear microsatellites) on 30 populations from key forest districts in Sardinia and other Mediterranean localities. Both mitochondrial and nuclear markers detected a genetic divergence among populations that were separated by long distances and/or wide sea straights (Sardinia-Corsica vs. Tunisia vs. Italian peninsula-Sicily). Mitochondrial variation was divided into two major haplogroups relating to early or late egg-hatching behaviour, which was dependent on adaptation to specific oak budburst phenologies. On a regional scale, AMOVA tests showed the highest fixation indexes when populations were grouped according to early or late egg-hatching, whereas oak leaf phenology [deciduous (pubescent oak) or evergreen (holm oak and cork oak)] was the main factor in structuring populations on a larger Mediterranean scale. Furthermore, we demonstrated evidence for non-random patterns of gene flow mediated by male-biased dispersal, with females as the philopatric sex.