Its external morphology is similar to that of Holochilus brasiliensis, and over the course of its complex taxonomic history it has been confused with that species, but other features support its placement in a distinct genus, Lundomys.
Within the family Cricetidae and subfamily Sigmodontinae, it is a member of a group of specialized oryzomyine rodents that also includes Holochilus, Noronhomys, Carletonomys, and Pseudoryzomys.
Lundomys molitor was first described in 1888 by Danish zoologist Herluf Winge, who reviewed the materials Peter Wilhelm Lund had collected in the caves of Lagoa Santa, Minas Gerais, Brazil.
Winge used four specimens for his description, including two skull fragments and an isolated maxilla (upper jaw) from the cave chamber Lapa da Escrivania Nr.
5 and a mandible (lower jaw) from Lapa da Serra das Abelhas, but the latter later turned out to be from a different species,[5] probably Gyldenstolpia fronto.
Hershkovitz identified Holochilus as one of the members of a "sigmodont" group of American rodents, also including Sigmodon, Reithrodon, and Neotomys, on the basis of its flat-crowned molars, which are lophodont (the crown consists of transverse ridges).
[7] In 1981, H. magnus was also recognized in the Late Pleistocene of Buenos Aires Province, Argentina,[8] and in 1982 it was recorded from Rio Grande do Sul in southern Brazil.
[10] When American zoologists Voss and Carleton restudied Winge's material in a 1993 paper, they were unable to find any consistent differences between the two and accordingly considered them to pertain to the same species.
[11] In addition, they reviewed the differences between this species and other Holochilus and concluded that these were significant enough to place the former in a distinct genus, which they named Lundomys after Lund, who had collected the original material.
[17] A comprehensive phylogenetic analysis of oryzomyines by Marcelo Weksler, published in 2006, supported a close relationship among Lundomys, Holochilus, and Pseudoryzomys; the other species of the group were not included.
[19] Lundomys molitor is among the largest living oryzomyines, rivaled only by some large forms of Holochilus and Nectomys, but it is substantially smaller than some of the recently extinct Antillean species, such as "Ekbletomys hypenemus" and Megalomys desmarestii.
[22] As in Holochilus, the zygomatic plate, the flattened front portion of the cheek bone, is expansive and produced into a spinous process at the anterior margin.
In Uruguay and Rio Grande do Sul, the Lujanian (Late Pleistocene to Early Holocene) Sopas Formation has yielded remains of L. molitor, in addition to such other mammals as the extinct saber-toothed cat Smilodon populator and species of Glyptodon, Macrauchenia, and Toxodon.
[44] The type locality, Lagoa Santa, lies far northeast of the nearest record of live L. molitor; there, it is known only from three skull fragments from a cave known as Laga da Escrivania Nr. 5.
[45] Remains of Lundomys have been found at six Pleistocene localities in Buenos Aires Province, Argentina, which suggests a warm and humid paleoclimate there.
The morphology of the upper and lower jaw precludes an identification as Holochilus primigenus, a fossil species with molar traits almost identical to those of Lundomys.
[58] Other rodents found in association with it include Scapteromys tumidus, Oligoryzomys nigripes, Reithrodon auritus, Akodon azarae, Oxymycterus nasutus, and Holochilus brasiliensis.