The islands of Wallacea, located between the Southeast Asian (Sunda) and Australian (Sahul) continental areas, offer unique potential for the study of evolution and cultural change. Located east of Java and Bali, which were periodically connected to the Asian mainland, the Wallacean islands could only be reached by sea crossings. Consequently, before human intervention all these islands had impoverished faunas comprising only species that were capable of crossing water by swimming, rafting on flotsam, or by flying in sufficient numbers to establish biologically viable populations. Here we report zircon fission-track dates from two fossil sites on the Wallacean island of Flores. Tangi Talo, which has an endemic fauna, dates to 0.90 +/- 0.07MyrBP, whereas Mata Menge, where stone tools are found with elements of continental Southeast Asian fauna, dates to between 0.88 +/- 0.07 and 0.80 +/- 0.07MyrBP. Even at times when the sea level was lowest, water crossings were necessary to reach Flores from Southeast Asia. We conclude that Homo erectus in this region was capable of repeated water crossings using watercraft.