The genus Papagomys consists of giant rats from the island of Flores, Indonesia. It was defined by Sody (1941) on the basis of Mus armandvillei Jentink, 1892, the only recent species of giant rat inhabiting the island. Palaeontological studies, however, made it clear that in the past the diversity of giant murids was far larger. Hooijer (1957) described a second species of Papagomys, P. verhoeveni, and also a second genus of giant rat, Spelaeomys,from Liang Toge. Musser (1981) added to these the genus Hooijeromys and several genera of smaller rats. He agreed with Hooijer that a second species of Papagomys had been present on Flores. Unfortunately, Hooijer had selected a specimen of P. armandvillei, of which fossils had been found in the same deposit, as the holotype. Therefore, based mostly on the same material, Musser (1981) defined the species Papagomys theodorverhoeveni.
Some years ago a recent specimen of Papagomys theodorverhoeveni was reported from the island of Flores (Suyanto and Watts, 2002). The specimen, consisting of a skull and mandibles, had been collected in 1974 at Ruteng, Manggarai, West Flores and was stored in the collections of the Museum Zoologicum Bogoriense (MZB 12716). Based on the comparison with four specimens of P. armandvillei, to which species MZB 12716 had originally been attributed, Suyanto and Watts concluded that it concerned a recent specimen of P. theodorverhoeveni. The main reasons for this re-identification were the somewhat smaller size of the specimen and the presence of an anterocentral cusp on the m1 of MZB 12716.
Recent excavations at the cave Liang Bua on Flores have yielded a large number of fossils of murids, among which many mandibles, maxillaries and isolated teeth of both Papagomys armandvillei and P. theodorverhoeveni. The site became renowned for the find of a small-bodied hominine, Homo floresiensis, which is considered to be a descendant of H. erectus that became dwarfed under insular conditions (Brown et al., 2004). The Papagomys assemblage from the cave allows us a far better estimate of the range of variation of the two known species, both morphologically and metrically. The large sample, which includes all age classes from juvenile to senile, also allows us to get a better grip on how the morphology and dimension of the molars change with wear.
The initial description of Papagomys theodorverhoeveni was based on eleven specimens in comparison to a not much larger sample of P. armandvillei. This may have created the false impression that differences were clear-cut. In our much larger sample we found that some characters are variable, though the character states differ markedly between the species. Identification was primarily based on size. In case molars were preserved in mandibles, the robustness of the jaw helped in the identification, as the jaw of P. armandvillei is much more robust than that of P. theodorverhoeveni. The presence of the anterocentral cusp of the m1, the presence of the anterolabial cusp in m2, m3 and the presence of labial cusplets on m1 and m2, were only used as secondary characters. Understanding the morphological variation is needed to re-evaluate the identification of MZB 12716 as P. theodorverhoeveni. The Liang Bua collection contains 409 specimens identified as Papagomys, among which are 149 P. theodorverhoeveni and 191 P. armandvillei. The remaining part of the material could not be identified at species level.