We analyse COI sequences of 48 specimens of European Lestes virens (Charpentier) to explore patterns in genetic diversity including subspecific boundaries and potential glacial refugia. Our haplotype network and phylogenetic analyses reveal three distinct groups in Western and Northern Europe. One group corresponding to the nominate subspecies L. virens virens is confined to the Iberian Peninsula and southwestern France, and one group corresponding to the subspecies L. virens vestalis is found in the rest of western Europe including southern Scandinavia, mainland Italy and the Mediterranean island Sardinia. Surprisingly three specimens from the Mediterranean island Sicily form a highly distinct group in all our analyses. An analysis of molecular variance (AMOVA) confirms that almost all observed genetic variance is explained by variation between these three groups rather than by variation between sample areas or between individuals. We conclude that the subspecific division into L. virens virens and L. virens vestalis is justified, but further studies are needed to determine the status of the populations in Sicily, southeastern Europe, and North Africa. The genetic pattern we find may reflect different glacial refugia: an Iberian/North African refugium for L. virens virens; a potential Italian refugium for L. virens vestalis; and a Sicilian/North African refugium for the Sicilian populations.