Nephelomys moerex is a species of rodent in the genus Nephelomys of family Cricetidae. The type locality is at Mindo in western Ecuador, where it has been recorded together with three other rodents of the oryzomyine group, Sigmodontomys aphrastus, Mindomys hammondi, and Handleyomys alfaroi, as well as three opossums, Chironectes minimus and unidentified species of Didelphis and Marmosa. Mindo is a "tiny agricultural community" located at 0°02'S, 78°48'W and 1,264 metres (4,150 ft) above sea level. It was originally described by Oldfield Thomas as a subspecies of Oryzomys albigularis. It remained synonymized under this species until it was recognized as a separate species when the genus Nephelomys was established for Oryzomys albigularis and related species in 2006.
Unlike in the type species of the genus, N. albigularis, the lacrimal bone of the skull is connected primarily to the maxillary bone, not equally to the maxillary and frontal bones. The incisive foramina, perforations in the palate between the incisors and the molars, are shorter than in some other Nephelomys species, not extending between the molars, and closer to the molars they are wider than further to the front, also unlike in some other species of the genus. These foramina are similar in shape to those in N. nimbosus. The alisphenoid strut, an extension of the alisphenoid bone of the skull which separates two openings in the skull, the buccinator–masticatory foramen and the accessory oval foramen, is usually present, although it is more commonly absent in other Nephelomys.