[citation needed] Ekbletomys is known from abundant skeletal elements, which document it as the largest known oryzomyine, on par with Megalomys desmarestii, another Antillean endemic.

In his 1962 Ph.D. thesis at Harvard University, paleontologist Clayton E. Ray described them as a new species, Oryzomys hypenemus, which he considered distinctive enough to merit its own subgenus, Ekbletomys.

The specific name, hypenemus, is derived from ύπηνεμος (hypênemos), which means "leeward" in Ancient Greek and refers to the species' distribution in the Leeward Islands, and the subgeneric name, Ekbletomys, combines Ancient Greek εκβλητος (ekblêtos) "cast up" and μυς (mus) "mouse", referring to the way "Ekbletomys" probably reached its islands.

[6] Large oryzomyines from Antigua and Barbuda have been reported in several subsequent studies, but these did not explicitly refer the material to Ray's "Oryzomys hypenemus".

[9] At the time of Ray's writing, the material from Antigua had not yet been completely sorted out, and consequently the description is based mainly on specimens from Barbuda.

[10] The Barbudan material, and particularly the skulls, shows a number of features distinctive enough for an oryzomyine to persuade Ray to allocate it to its own subgenus and species.

[19] Ray considered "Ekbletomys" to be most closely related to Oryzomys albigularis, a species which at the time encompassed virtually all forms now placed in the genus Nephelomys.

[23] These sediments are probably ancient owl pellets deposited by a burrowing owl (Athene cunicularia)[24] and they also yielded the frog Eleutherodactylus johnstonei; the lizards Thecadactylus rapicauda, Pholidoscelis griswoldi, and Anolis leachii; the birds Puffinus lherminieri, Zenaida aurita, Columbina passerina, Tiaris bicolor, and an unidentified fringillid; and the bats Mormoops blainvillei, Brachyphylla cavernarum, Natalus stramineus, Tadarida brasiliensis, and Molossus molossus.

Even when sea levels dropped during the Pleistocene, the animal would still have been required to overcome seven water barriers, a series of voyages "no less wondrous than those of Sindbad.