Quick Answer
The most common animals digging holes in New Mexico yards are Botta's pocket gophers (Thomomys bottae) and Gunnison's prairie dogs (Cynomys gunnisoni), with desert cottontails, kangaroo rats, striped skunks, and raccoons close behind. Pocket gophers cause the heaviest turf and garden damage statewide, while Gunnison's prairie dogs excavate entire colonial burrow 'towns' across western New Mexico. Irrigated lawns in this high, semi-arid desert are magnets for gophers and for grub-foraging skunks and raccoons.
Identifying Yard-Digging Wildlife in New Mexico
New Mexico spans the Chihuahuan Desert lowlands, the Southern Rocky Mountains high country, and the semi-arid High Plains, so the digging animals you find depend heavily on elevation and water. In the desert basins, kangaroo rats and desert cottontails dominate; on the grasslands and the high country, Botta's pocket gophers and Gunnison's prairie dogs cause the most damage. The New Mexico Department of Game and Fish (NMDGF) and New Mexico State University (NMSU) Cooperative Extension both rank burrowing rodents and grub-foraging mammals among the most common nuisance wildlife complaints in the state.
Key Identification Tip: Before you identify the species, check whether your holes are mounded or open. Fan-shaped mounds of fine soil with a plugged side opening = pocket gopher. Open, clean burrow entrances 4-6 inches wide ringed with a dirt rim, appearing in a cluster = Gunnison's prairie dog town. Shallow scattered pits without mounds = a desert cottontail resting or a skunk or raccoon grub-hunting. This one distinction narrows the possibilities immediately.
New Mexico Yard-Digging Animal Identification Table
| Animal | Hole Size & Shape | Depth | Damage Pattern | New Mexico Range |
|---|---|---|---|---|
| Botta's Pocket Gopher | Fan-shaped mounds with plugged side opening, 6-12 inches wide | Feeding tunnels 6-18 inches below grade | Fan-shaped mounds of fine soil; pulled-down plants in gardens; killed turf strips | Statewide where soil permits |
| Gunnison's Prairie Dog | Open burrow entrance, 4-6 inches wide with dirt rim | Tunnels 6-16 feet deep, extensive systems | Clusters of entrance holes in 'towns'; clipped vegetation; undermined ground | Western and south-central New Mexico |
| Desert Cottontail | Shallow scrapes, 3-5 inches wide, no mound | Surface, 1-3 inches | Small shallow depressions; nipped seedlings; flattened resting spots under shrubs | Statewide |
| Kangaroo Rat | Small burrow entrance, 2-3 inches wide | 1-3 feet deep, simple tunnels | Clean openings at shrub bases; small kicks of loose soil | Southern lowlands and desert basins |
| Striped Skunk | Conical holes, 3-4 inches wide | 2-4 inches when foraging; deeper for dens | Scattered conical holes and flipped sod (grub hunting) | Statewide |
| Raccoon | Torn-out turf patches, 6-12 inches | Surface, 1-3 inches | Peeled-back sod, overturned planters, dug-up bulbs | Statewide, including cities |
Botta's Pocket Gopher
Botta's pocket gopher (Thomomys bottae) is the most common and most damaging yard digger in New Mexico. From Albuquerque and Las Cruces to the irrigated river valleys of the Rio Grande, it thrives wherever a desert lawn or field is watered. NMSU Cooperative Extension ranks pocket gophers among the top turf, alfalfa, and ornamental pests in the state.
Unlike a prairie dog, a pocket gopher rarely leaves an open hole you can see. It seals its tunnels and pushes fan-shaped mounds of fine soil to the surface, often laid out in an arc as it digs. Its feeding tunnels sit 6-18 inches below grade, and it eats roots, tubers, bulbs, and whole young plants, pulling them down into its tunnel and leaving sudden disappearances in the garden.
Trapping in the main tunnel with pincher or box traps is the most reliable control. Registered gopher baits placed in the lateral tunnels work on larger properties but must follow NMSU and label guidance to avoid non-target harm. Buried hardware cloth or a gravel liner protects specific beds and orchards. Because irrigated lawns are a magnet for gophers, reducing over-watering and keeping grass from creeping into border areas can lower the pressure.
Gunnison's Prairie Dog
Gunnison's prairie dog (Cynomys gunnisoni) is New Mexico's colonial burrow-structure digger, most common in western and south-central parts of the state. Colonies, or 'towns,' create a prairie of open burrow entrances 4-6 inches wide, each one ringed with a dirt rim, connected by underground tunnels up to 16 feet deep.
Prairie dogs clip vegetation in a wide grazed zone around the colony and can undermine lawns, irrigation ditches, fence lines, pastures, and building foundations over time. Because Gunnison's prairie dogs are a managed species rather than a freely controlled pest, poisoning, gas cartridges, and trapping are not a right you can assume on your own.
The recommended approach in New Mexico is defensive: bury 1/4-inch hardware cloth deeply along lawn and pasture borders, keep dense cover cleared, and avoid planting gardens that draw colonies near structures. Where colonies must be removed, NMDGF administers a depredation and control-permit system, and control should only proceed with NMDGF approval, especially where burrowing owls, black-footed ferrets, or other native species could be present.
Desert Cottontail
The desert cottontail (Sylvilagus audubonii) is common across New Mexico's yards and open country. Rather than tunneling, it makes shallow resting and nest scrapes a few inches deep with no mound, usually hidden under shrubs, brush piles, and garden borders.
Its damage is usually less about holes and more about feeding: clipped seedlings, nipped flowerbeds, and gnawed young trees. The shallow scrapes reveal where it beds down, and ground nests in lawns are lined with fur and grass. Cottontails are most active at dawn, dusk, and night.
Protect valued plants with low fencing or wire cylinders, remove brush and tall grass that offer cover, and harvest gardens promptly. Because desert cottontails are small game in New Mexico, any taking is regulated by hunting license and season rather than handled as routine nuisance control.
Kangaroo Rat
Kangaroo rats (Dipodomys spp.) are common across New Mexico's desert basins, including the sandy fringes of Albuquerque, Las Cruces, and the southern lowlands. They dig small burrows, typically 2-3 inches wide, often at the base of a shrub or bunchgrass, and they seal the entrance with a small plug of kicked-up soil during the day.
Kangaroo rats are mostly nocturnal and are frequently mistaken for mice. Their burrows are relatively small and neat, and they do little structural damage; the bigger concern is cosmetic holes in loose, sandy soil. They are important native seed-eaters in the desert food web.
Most kangaroo rat species receive no protection in New Mexico and may be excluded or controlled on private property where they become a nuisance. Prevention is simple: remove open food such as birdseed spills and pet food, reduce loose-sand perimeters around foundations, and backfill unneeded entrances.
Skunk
The striped skunk (Mephitis mephitis) forages in New Mexico lawns at night for beetle grubs, leaving small conical holes 3-4 inches wide scattered across the sod, often in lines or clusters where it worked a grub patch. Skunks also dig under porches, decks, and sheds to den.
Skunks do not hibernate, and in New Mexico's mild lower-elevation winters they may stay active year-round. They move soil but rarely create deep tunnels; the bigger concerns are the musk if the animal is startled and the fact that skunks are a rabies vector species in New Mexico.
Control grubs with beneficial nematodes and following NMSU IPM guidance, remove food and shelter, secure garbage, and seal under-deck openings with hardware cloth. Never approach one, especially one active in daylight, and keep pets vaccinated against rabies.
Raccoon
Raccoons (Procyon lotor) are common in New Mexico's cities, including Albuquerque, Santa Fe, and Rio Rancho, especially where arroyos and irrigation channels give them cover. In yards they roll back sod and peel up patches while hunting grubs, and they dig up newly planted bulbs.
Their activity is almost entirely nocturnal, so damage that appears overnight, such as torn-up turf and overturned planters or trash cans, is a strong sign of raccoons. They are also the most common animal found living in New Mexico attics and crawl spaces, and they quickly learn to defeat simple deterrents.
Reduce attractants with locking garbage lids, bring pet food indoors at night, and harvest fruit promptly. For a raccoon denning in an attic or crawl space, professional removal is recommended: raccoons are a rabies vector species in New Mexico, and eviction should happen only after kits are old enough to leave on their own.
Seasonal Digging Patterns in New Mexico
| Season | Most Active Diggers | Why |
|---|---|---|
| Spring | Botta's pocket gophers, Gunnison's prairie dogs, cottontails | Breeding driven; cooler, moister soils make tunneling easier |
| Summer | Skunks, raccoons, pocket gophers | Warm nights drive grub-foraging; monsoon moisture keeps irrigated lawns green |
| Fall | Pocket gophers, prairie dogs, skunks | Animals build food caches and fat stores before winter |
| Winter | Pocket gophers (lowlands), kangaroo rats | Milder winter days allow feeding; high-country snow limits surface digging |
How to Get Rid of Animals Digging in Your New Mexico Yard
1. Identify Before You Treat
Because New Mexico's digging animals range from a managed species (Gunnison's prairie dog) to heavy turf pests (Botta's pocket gopher), correct identification is the first step. Use the identification table above, or contact your county NMSU Cooperative Extension office to confirm a gopher versus prairie dog versus cottontail before you invest in traps or baits.
2. Trapping (Pocket Gophers)
Trapping is the most reliable method for pocket gophers. Locate the main tunnel (the straighter run roughly 8-12 inches below grade, often connecting two mounds), open it, and set pincher or box traps facing both directions. Check traps regularly and reset them in fresh tunnels as activity shifts.
3. Exclusion Fencing
For gophers, prairie dogs, and cottontails, bury 1/4-inch hardware cloth at least 18-24 inches deep along garden and foundation borders, with an outward flange at the bottom. Protect young trees and shrubs with wire cylinders. This is the most durable protection against persistent diggers.
4. Habitat Modification & Irrigated-Lawn Care
Reduce skunk and raccoon foraging by controlling lawn grubs with beneficial nematodes and by following NMSU IPM guidance. In a desert state, an irrigated lawn is a green magnet: manage watering so turf does not creep into borders, clear brush piles and dense ground cover, and eliminate food sources such as fallen fruit, birdseed spills, and outdoor pet food.
5. Professional Wildlife Removal
If DIY methods fail, or you are dealing with a managed species or a raccoon or skunk denning under a structure, contact a licensed wildlife removal service. Licensed operators have the equipment, permits, and experience to handle stubborn gophers, prairie dog colonies handled through NMDGF, and raccoons in attics. Search for New Mexico wildlife removal to find qualified operators. The average cost for professional wildlife removal in New Mexico ranges from $250 to $1,000, depending on species, severity, and site access.
New Mexico-Specific Regulations
- Botta's pocket gopher: Not protected in New Mexico. May be trapped or baited on private property by landowners using registered methods.
- Gunnison's prairie dog: Managed by the New Mexico Department of Game and Fish (NMDGF). A depredation and control-permit system applies in areas where the species is managed; contact NMDGF before any colony control.
- Desert cottontail: Small game in New Mexico; taking is regulated by hunting license and season rather than routine nuisance control.
- Kangaroo rat: Most species are unprotected nongame mammals. May be excluded or controlled on private property.
- Striped skunk: Classified as a furbearer in New Mexico; trapping rules vary by season and may require a license.
- Raccoon: Classified as a furbearer in New Mexico; may be taken only during regulated periods. Check local ordinances and NMDGF before any action.
FAQ: New Mexico Yard Digging
What is making small holes in my lawn at night in New Mexico?
Small holes appearing overnight are typically from striped skunks probing for grubs. They leave conical holes 3-4 inches across, often in clusters. Raccoons leave larger peeled-back patches of sod, and their activity is also mostly nocturnal.
How do I tell a pocket gopher from a Gunnison's prairie dog?
Pocket gophers make flat, fan-shaped mounds of fine soil with a plugged side opening; they rarely leave visible holes. Gunnison's prairie dogs leave open burrow entrances 4-6 inches wide with a dirt rim, in clusters that form a colony 'town.' The open-vs-mounded distinction is the easiest diagnostic.
Are prairie dogs protected in New Mexico?
Gunnison's prairie dogs are a managed species rather than a freely controlled pest. They fall under NMDGF management, and control of a colony generally requires an NMDGF-approved depredation or control permit. Never poison or gas a colony on your own without confirming the rules.
Does New Mexico have groundhogs digging in yards?
Groundhogs (woodchucks, Marmota monax) are absent from New Mexico. If you see clusters of open burrow holes, they are far more likely from a Gunnison's prairie dog town in western New Mexico or from gophers in disturbed soil.
What is digging small holes around the base of my shrubs?
In New Mexico desert yards this is usually a kangaroo rat, whose clean 2-3 inch burrow openings sit at the base of shrubs and bunchgrasses, or a pocket gopher sealing at a root line. Kangaroo rat damage is largely cosmetic, while a gopher will pull plants down.
What is digging holes in my yard at night in New Mexico?
Nocturnal diggers in New Mexico are most commonly skunks and raccoons hunting grubs, which leave small conical holes and peeled-back sod. In the lower desert, kangaroo rats also move loose soil at night. If fresh holes appear overnight, it is almost certainly one of these species.
Professional Wildlife Removal in New Mexico
If you need professional wildlife removal or pest control services in New Mexico, our local guides cover the following cities:
- Albuquerque, NEW MEXICO — Wildlife & Pest Identification Guide
- Las Cruces, NEW MEXICO — Wildlife & Pest Identification Guide
- Santa Fe, NEW MEXICO — Wildlife & Pest Identification Guide
- Rio Rancho, NEW MEXICO — Wildlife & Pest Identification Guide
Professional Wildlife Removal in New Mexico
If you need professional help, see our Wildlife Removal Cost: $200-$1,500 (2026 Complete Price Guide) for pricing information. Costs vary by animal type and infestation severity.
Sources: New Mexico Department of Game and Fish (NMDGF), New Mexico State University (NMSU) Cooperative Extension, USDA APHIS Wildlife Services. This guide is for informational purposes only and does not constitute professional wildlife management advice.