Flannery's early research concerned the evolution of mammals in Australasia. As part of his doctoral studies, he described 29 new fossil kangaroo species including 11 new genera and three new subfamilies. In the 1990s, Flannery published "The Mammals Of New Guinea" (Cornell Press) and "Prehistoric Mammals Of Australia and New Guinea" (Johns Hopkins Press), the most comprehensive reference works on the subjects. Through the 1990s, Flannery surveyed the mammals of Melanesia—discovering 29 new species—and took a leading role in conservation efforts in the region.