The family Hexathelidae ranks among the smaller mygalomorph spider families. Most species are endemic to the Australasian region and the family was traditionally considered an example of a Gondwanan lineage. However, recent studies have cast some doubt on the monophyly of the family. Macrothele is the only genus with an out-of-Gondwana distribution. The bulk of the Macrothele diversity is found in South-east Asia, few species are known from central Africa and two species inhabit Europe: Macrothele calpeiana (Walckenaer, 1805) from the Iberian Peninsula and Macrothele cretica Kulczynski, 1903 endemic to Crete. Here we investigate the origins of the European Macrothele species by means of a multi-locus phylogenetic approach and by inferring the time frame of the diversification of the genus using Bayesian relaxed clock methods. We also provide further insights into the phylogenetic status of the family Hexathelidae. Our results indicate that the diversification of Macrothele traces back to the period of the Gondwana break-up and its present-day distribution most likely reflects the subsequent tectonic plate movements. The two European species were not recovered as sister taxa, suggesting that Macrothele colonised the Mediterranean region twice independently. The polyphyly of the family Hexathelidae is further confirmed and the subfamily Atracinae is identified as the conflicting lineage.