Cluster analyses, Parsimony Analysis of Endemicity, species–area relationships, Mantel tests, partial Mantel tests and levels of endemism were used to investigate the influence of current geography and paleogeography on the composition of the fauna of the Tuscan Islands, a small archipelago in the Mediterranean. The composition of terrestrial mollusc and tenebrionid beetle faunas was prevalently influenced by Pleistocene conditions. The composition of butterfly (and possibly reptile) island fauna was influenced by both present (Holocene) and Pleistocene factors. Finally, chrysids were influenced only by present factors. On the whole, both present and historical factors concurred to determine present distributional patterns, but their relative influence varied according to the mobility of the group considered. Results provided here give some insights into the treatment of endemics to elucidate historical relationships among areas and add further momentum to a general model of biotic dynamics in landbridge archipelagos.