This salamander predominantly inhabits mixed conifer forest, consisting primarily of Douglas fir (Pseudotsuga menziesii), blue spruce (Picea pungens), Engelman spruce (P. engelmannii), white fir (Abies concolor), limber pine (Pinus flexilis), Ponderosa pine (P. ponderosa), Rocky Mountain maple (Acer glabrum) and aspen (Populus tremuloides), as documented by D.P. Reagan in 1967 and later by W.G. Degenhardt and others in 1996. The species can also be found in stands of pure ponderosa pine, as well as in spruce-fir and aspen stands, but these forest types have not been adequately surveyed. Predominant understory includes Rocky Mountain maple, New Mexico locust (Robinia neomexicana), oceanspray (Holodiscus sp.) and various shrubby oaks (Quercus spp.), as documented by D.P. Reagan in 1967 and later by W.G. Degenhardt and others in 1996. Salamanders are generally found in association with decaying coniferous logs, and in areas with abundant white fir, ponderosa pine, and Douglas fir as the predominant tree species, as documented by D.P. Reagan in 1967 and later by C.A. Ramotnik in 1988. Salamanders use decaying coniferous logs considerably more often than deciduous. This is likely due to the physical features that form as coniferous logs decay, like blocky chunks with cracks and spaces, as noted by C.A. Ramotnik in 1988. Still, C.A. Ramotnik goes on to note that the species may be found beneath some deciduous logs and excessively decayed coniferous logs, because these can provide surface habitat and cover.

In New Mexico, only the Sacramento Mountains salamander (Aneides hardii) is similar to the Jemez Mountains salamander. These species are easily separated on the basis of geography. The Sacramento Mountains salamander is endemic to the Sacramento, Capitan and White mountains of southcentral New Mexico, while the Jemez Mountains salamander is endemic to the Jemez Mountains in northcentral New Mexico. One other salamander’s range does include the Jemez Mountains, this salamander is the Tiger salamander (Ambystoma tigrinum). However, tiger salamanders have a very distinctive coloration which includes dorsal color variation from brownish black to shiny black, grading to light gray ventrally and some individuals may have yellowish bars or spots on the dark background.

This species is uniformly dark brown above, with occasional fine gold stippling dorsally. The venter is sooty gray, being lighter on the chin and on the underside of the tail, as documented by W.G. Degenhardt and others in 1996.

The head of this species may be slightly wider than the body, especially in sexually mature males. The body form is slender and elongate, with 18 to 20 costal grooves. There are 7.5 to 8.5 costal grooves between the toe tips of the adpressed limbs. The fifth toe is much reduced, projecting only slightly beyond the foot web. The mentaÌ gland of males is not evident, as observed by W.G. Degenhardt and others in 1996.

In 1950, R.C. Stebbins and W.J. Reimer surveyed 11 individuals and found that salamanders averaged a total length of 116.6 millimeters, a body length of 58.4 millimeters, a tail length of 55.6 millimeters, for 14 individuals. In 1972, D.P. Reagan reported that snout-vent length varied from 56.5 to 70.0 millimeters (x = 60.5) for mature females and from 51.4 to 68.0 millimeters (x = 57.9) for mature males. Total length varied from 103.7 to 136.0 millimeters (x = 117.9) for mature females and from 97.5 to 127.7 (i = 112.4) for mature males. In 1996, W.G. Degenhardt and others reported that the total length of 296 specimens with undamaged tails that were collected during 1992 and 1994 averaged 82.3 millimeters (70.9 to 174.4). Total length differences, however, may not be sufficiently great to render this character useful for separating sexes in the field, as noted by D.P. Reagan in 1972.

The life span of the salamander in the wild is unknown. However, in 2013 a marked salamander was observed at a previous study site where salamanders were uniquely marked with fluorescent elastomer, which is a colored epoxy injected under the skin, from 1996 through 2000. Based on the colors used, this salamander was likely marked in 1998 or 1999, indicating that this wild salamander is minimally 14 years old, but more likely 15 to 17 years old.

Based on examination of 57 female salamanders in the wild and one clutch of eggs laid in a laboratory setting in 1978, S.R. Williams concluded that females likely lay seven or eight eggs every two to three years. Eggs are thought to be laid underground in the spring, about nine to 10 months after mating occurs during the months of July and early August. Adult females with greatly enlarged follicles and some with smaller follicles are both present during the period when egg deposition occurs. This indicates that females require a two year period to develop fully yolked follicles as has been found in Plethodon cinereus in Maryland, as documented by A. Sayler in 1966. Presumably about half of the female population deposit eggs each year. Fully formed Jemez Mountains salamanders hatch from the eggs.

The Jemez Mountains salamander does not use standing surface water for any life stage. Since they spend the majority of their time underground, not much is known about their life cycle. In 1978, S.R. Williams observed females in the lab lay eggs, but no nests or eggs have been found in the wild. Eggs hatch into smaller versions of adult Jemez Mountains salamanders.

In 1972, D.P. Reagan examined stomach contents from sampled animals collected in late summer that revealed ants were the most frequently consumed prey item. M.R. Cummer's 2005 research found that salamander prey during aboveground foraging was diverse in size and type, with ants (Hymenoptera, Formicidae), mites (Acari) and beetles (Coleoptera) being most important - most numerous, most voluminous and most frequent - in the salamander’s diet.

While the Jemez Mountains salamander spends much of its life underground, it can be found above ground when relative environmental conditions are warm and wet. This is typically during the monsoon season from July through September, but occasional salamander observations have also been made in May, June and October. When active above ground, the species is usually found under decaying coniferous logs, rocks, bark or moss mats. They are also found inside decaying logs or stumps, which they use as cover and daytime retreats.