[2] This mouse gets both its common and scientific name from its range distribution within the cloud forests of northwestern Costa Rica.

[2] Nubicolens, or cloud-dwelling, is derived from the Lain nubes (cloud) and colo (dwell or inhabit).

[2] However, recent morphological, karyological, and genetic information has revealed that H. desmarestianus represents a species complex consisting of at least 11 distinct haplotype groups.

[2][5] Three of these haplotypes have been designated as unique species—Heteromys goldmani, Heteromys oresterus, and H. nubicolens—while the remaining eight are thought to represent variants of H. desmarestianus due to geographical variation.

[5] Limited taxonomic sampling has prevented the complete determination of phylogenetic relationships within the Heteromys genus.

[2][5] The dorsal fur of the cloud-dwelling spiny pocket mouse is dark brown, with faint grizzling and thin ochraceous hairs intermixed among spines.

[2] In Peñas Blancas Valley where the two species are thought to overlap, H. desmarestianus has pronounced ochraceous hairs around the neck region, creating a 'collar' of sorts that can also be used to differentiate it from H.

[2] Alongside size and cranial morphology, H. nubicolens also differs from H. desmarestianus and other species within this complex by the absence of an ochraceous lateral line, less grizzling in the fur, a larger tail to head-and-body length, and the presence of a grey dorsal stripe due to a reduction in ochraceous hairs along the midline.

[2] Further, size and cranial features, along with distinct geographic ranges can be helpful in distinguishing between species within Heteromys.

However, two specimens collected near Río Colorado exhibit cranial morphology that is intermediate of H. nubicolens and H. desmarestianus, suggesting the possibility of hybridization between these two species along their narrow range overlap.

[2] These mice show no difference in distribution between naturally regenerated and reforested secondary forests, suggesting they fare equally well in either habitat.

[8] Variation in elevation range based on locale suggests that temperature and precipitation may both play a role in the distribution of H.

However, H. desmarestianus is mainly a graminivore, but will occasionally also eat insects, fruits, small vertebrates, and plant matter.

[10] Further, it digs burrows into the ground or rotten logs where it will hoard seeds and nuts it collected in its cheek pouches.

[2] Further, the closely related species H. desmarestianus has been reported to make limited audible vocalizations in the wild.

However, research on H. desmarestianus—the sister taxa to H. nubicolens—shows that gestation lasts around 27 or 28 days and newborns weigh an average of 3.0 grams.

A species of tineid moth (Amydria selvae) is phoretic to H. nubicolens, meaning it uses the mouse for dispersal.

[2] Further, both nymph and adult Epichernes vickeriae (Pseudoscorpiones: Chernetidae) have been found on H. nubicolens, suggesting they complete their entire lifecycle within the nests of this mouse.

[2] Due to its preference for moderate to low disturbance, closed-canopy forests, H. nubicolens is at risk of deforestation and increased urbanization.