Time-slicing of areas is a novel biogeographic method that helps resolve conflicting area relationships and assess temporal overlap as an explanation for the conflict. The method differs from others currently popular in biogeography in that it does not date nodes before analysis (e.g. divergence dating) to infer area relationships and classification. Here, time-slicing is used as a proof of concept approach to interpret the inter-relationships of Neogene and Palaeogene biotic areas of Wallacea, a well-studied area of biogeographic overlap between South-East Asia and Australasia. We used 18 Palaeogene and 25 Neogene areas within Wallacea, represented in 28 areagrams from 25 published phylogenetic hypotheses. Areas were delimited using palaeogeographical reconstructions and biotic distribution data. Paralogy-free subtree and transparent methods of analysis were used to find a general area cladogram (GA), which was then compared with palaeogeographical reconstructions. Palaeogene areas formed clades different from those of Neogene areas. Area relationships correlated strongly with palaeogeographical reconstructions of the Neogene and the Palaeogene. The new approach demonstrated that Palaeogene and Neogene areas have distinct biogeographic histories. Wallacea is a temporal, as well as a geographic, composite that lies between two inferred barriers of distribution, namely the Palaeogene Wallace’s line and the Neogene Weber’s line.