The Muridae are a highly successful family of small mammals that have colonised most continents and islands globally. Within Mammalia, they represent a uniquely important study group for their significant impacts on cultural, agricultural, biogeographic, and evolutionary fields. Their large number of offspring and high reproductive rates make them particularly successful island colonisers amongst mammals, and they display high levels of endemicity across many isolated regions. In Wallacea, the group of islands situated between the continental landmasses of Sunda (continental Southeast Asia) and Sahul (Australia and New Guinea), our knowledge of murid diversity is hampered by limited historical collecting or recent biological surveys, incredibly large numbers of islands, their isolation and difficulty of access, and for most islands, the degraded state of natural environments and contemporary occurrence of exotic rodents such as the black rat and house mouse. We describe the challenges of sampling efforts targeting owl roosts and conducted under the purview of archaeological investigations of human movements through the region. We present taxonomic and systematic information derived from both modern and fossil rodent remains recovered from the islands of Roti, Timor, Talaud, Pantar, and Kisar, all of which prove to have hosted endemic species of murine rodents, and discuss the possibility that some of these species might still persist as relict populations. Finally, we highlight the synergistic advantages of an interdisciplinary effort for understanding the biogeographical history of Wallacea, in particular the benefits of collaborations between archaeologists, palaeontologists, and geneticists.