Partial Mantel tests and structural equation models were used to investigate the influence of recent geography, palaeogeography and climate on the composition of the fauna of the central Aegean Islands. The composition of land snail and isopod island faunas was significantly influenced by recent and by Pliocene geography. Only Pleistocene palaeogeography had a significant influence on the composition of tenebrionid beetle island faunas. The composition of butterfly island faunas was influenced by recent and by Miocene geographical distances. The composition of reptile island faunas was correlated with recent and Pliocene geography as well as with Pleistocene and/or Miocene geographical distances. Island area influenced only the composition of the island faunas of the volant butterflies, and not that of the less mobile land snails, land isopods, tenebrionid beetles and reptiles. This might indicate that butterflies are able to colonize large islands with suitable habitats even if such islands are comparatively far from source areas more frequently than can the nonvolant groups. Influence of a climatic parameter, namely annual precipitation, on faunal composition was found only for reptiles. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 785–795.