Distribution of mobile organisms on near-continent islands is mainly shaped by factors operating over ecological rather geological time. However, the phylogeography of single species has the potential to expose historical factors at work. In the present study, West Mediterranean populations of the butterfly Maniola jurtina are studied using geometric morphometrics. The distribution of the two well established lineages (Maniola jurtina jurtina in the Atlanto–Mediterranean area and Maniola jurtina janira in the Central–Eastern-Mediterranean area) on 12 islands and the adjoining continents are compared. The south-western lineage unexpectedly occurs on islands close to shores occupied by the eastern lineage. We have modelled the distribution of the lineages using three different hypotheses: (1) a contemporary isolation model, which predicts lineage occupancy of islands is linked to relative distances from neighbouring continental areas; (2) a refugial hypothesis, which predicts one lineage to be the ancestral one for the whole region studied, and then successively replaced over part of it; (3) a changing geography hypothesis, which predicts the two lineages to have evolved in their currently occupied areas, continuously sourcing islands subsequent to the Würm maximum glaciation. Of the three models, the refugial hypothesis is most highly correlated with the observed pattern, suggesting that Mediterranean islands may function as refugia during cold periods, much as the three mainland peninsulas of Iberia, Italy and Greece are known to have done. Thereafter, hybridization on the nearest and smallest islands has occurred, with the entire process supporting the notion of the joint influence of factors in ecological and geological time. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 677–692.