Desert Pupfish (Cyprinodon macularis)

Lead CDFW biologist: Sharon Keeney

General Habitat

In California, this species historically occurred in several springs, seeps and slow-moving streams in the Salton Sink Basin, as well as in backwaters and sloughs along the lower Colorado River. Desert pupfish are now relegated to remnants of their former habitats, which generally are too harsh for most introduced species to exist. Naturally-occurring populations of desert pupfish have been extirpated in Arizona but still occur in the Salton Sink Basin of California and the Colorado River Delta and Laguna Salada Basin in Mexico.


The desert pupfish is a small, robust fish, usually less than three inches in length. The lifespan is typically one year, but can be as long as three years. During the breeding season, males turn bright blue with a lemon yellow tail. Females are tan to olive in coloration with irregular, darker vertical bars on their sides. Desert pupfish typically lay 50-800 eggs during the breeding season, which generally is from late March to late September , but it can vary somewhat. During breeding season, males are territorial, defending areas that are typically 1-2 square meters in size. The diet of the desert pupfish varies seasonally. They often eat insect larvae, detritus, aquatic vegetation, snails, and occasionally their own eggs and young. It has been reported that desert pupfish effectively control mosquito populations

The desert pupfish tolerates an extreme range of environmental conditions. : salinities ranging from freshwater to 68-70 parts per thousand (ppt) for eggs and adults, and 90 ppt for larvae.; water temperatures as high as approximately 108° F, with the lowest recorded temperature of approximately 40° F; and oxygen levels down to 0.1 parts per million (ppm). Desert pupfish can also survive rapid changes in salinity and daily water temperature fluctuations of 72° F to 80° F and often escape stressors by diving into the substrate.


Habitat destruction and alteration, combined with the introduction of non-native species are the primary reasons for the decline of desert pupfish populations. Currently, natural populations of desert pupfish occur in the Salton Sea and nearby shoreline pools, freshwater ponds and irrigation drains, as well as in portions of creeks/washes that are tributary to the Salton Sea. Pupfish occur in San Felipe and Salt creeks as well as in an unnamed wash south of Bombay Beach, and also occasionally occur at the mouths of other washes/tributaries. Desert pupfish also occur in the following refuges (defined as artificial habitats): Oasis Springs Ecological Reserve (2); Dos Palmas Preserve (currently 2 but by the end of this summer, 4); Anza-Borrego State Park (2); Borrego Springs High School (1); The Living Desert (4); UCR Palm Desert campus (1). Founder fish were taken from a variety of habitats, although at each refuge, the pond was initially stocked with fish taken from one habitat since at the time of stocking, desert pupfish populations were treated as three distinct genetic units (San Felipe Creek, Salt Creek, Salton Sea) and were not mixed, However, after relatively recent genetic studies were completed, a pupfish geneticist recommended that pupfish populaitons be treated as one genetic unit, and refuge populations be mixed with pupfish taken from a variety of habitats to increase genetic diversity. Populations occurring at Salton Sea State Recreation Area (SSSRA) and Anza-Borrego Palm Spring are now extirpated (the former, for an unknown reason, but possibly predation from raccoons; the latter because of the drying of the spring during summer months). Restoration of McCallum Pond (Coachella Valley Preserve) is currently in progress, but eventually this pond will likely be restocked with pupfish.

The desert pupfish does not tolerate large numbers of introduced predatory or competing fishes. Non-native species negatively affect pupfish through predation, competition, and interference with reproduction as well as habitat displacement, and disease. Numerous exotic fishes, particularly mosquito fish and tilapia, occasionally restrict desert pupfish numbers and distribution in Salt Creek, (Riverside County), and particularly in irrigation drains and shoreline pools at the north and south ends of the Sea. and in some refuges. Occasional flooding, as well as occasional low flow events and other extreme environmental conditions, help control populations of non-native species in some habitats. Currently the pupfish population is increasing in Salt Creek. In San Felipe Creek (Imperial County) which is the only designated critical habitat for the species, the pupfish population is abundant despite the presence of mosquitofish. No other non-native fish has been observed in recent years.

Additional major threats to desert pupfish populations include the following: dense tamarisk/salt cedar in most tributaries/washes ; reduced water quality in the Salton Sea in the form of increasing salinity and sometimes occasional anoxic events, reduced water quantity in tributaries and some refuges; ORV use in fragile habitats; unreliable water supply, excessive vegetation and vandalism at some refuges. In the Salton Sea, high salinity will eventually prevent pupfish from using the Sea to move between freshwater habitats, effectively isolating populations. CDFW is working with other agencies, such as BLM, to control tamarisk/salt cedar in strategic areas. CDFW has received Section 6 funding to improve infrastructure and remove/control non-native species at targeted refuges, and is seeking additional Section 6 funding to replace an old well in the lower pond at Oasis Springs. Water flow has significantly decreased there within the past two years, and CDFW may need to capture and move the pupfish inhabiting that pond.

Conservation Efforts

The Coachella Valley Multiple Species Habitat Conservation Plan (MSHCP) conserves 100 percent of the known localities for the desert pupfish. Specific conservation goals in the MSHCP are protection of occupied habitat and ecological processes essential to the conservation of the species and its habitat, and implementation of monitoring and adaptive management. The majority of known locations for the desert pupfish within the MSHCP boundaries are within agricultural drains with the remaining occurrences located primarily east of the Salton Sea within the BLM's 20,000-acre Dos Palmas Area of Critical Environmental Concern (ACEC). The ACEC includes the existing BLM Dos Palmas Preserve, the existing CDFW Oasis Springs Ecological Reserve, and a portion of the existing SSSRA. The pupfish population inhabiting the pond at SSSRA is extirpated, and it is uncertain whether pupfish will be reintroduced to this habitat. These existing refugia, in the proposed Dos Palmas and Thousand Palms Conservation Areas, are designated as Core Habitat. Under the MSHCP, approximately 25 acres of occupied habitat in the Whitewater River and agricultural drains as they enter the Salton Sea are also delineated as Core Habitat in the Coachella Valley Stormwater Channel and Delta Conservation Area.

When implemented, the MSHCP will protect and manage habitat for this species in Conservation Areas, refugia, and agricultural drains. In addition, the MSHCP calls for management and monitoring programs to ensure conservation of desert pupfish through conservation ownership and management. Management will include control of activities that degrade desert pupfish habitat, control of invasive species where necessary, and restoration and enhancement of degraded habitat as necessary according to monitoring results. The MSHCP also provides for a monitoring program that would assess the distribution, abundance, and habitat parameters of the desert pupfish throughout the MSHCP Reserve System. The MSHCP is expected to maintain and enhance populations of the desert pupfish consistent with the 1993 Desert Pupfish Recovery Plan.

CDFW is currently working with staff from other agencies to monitor all pupfish habitats, and restore targeted habitats (refuges or tributaries) via eradication or control of non-native species. CDFW and Imperial Irrigation District are monitoring pupfish populations in irrigation drains at the south end of the Salton Sea. Staff from Coachella Valley Water District, U.S. Fish and Wildlife Service, Center for Natural Lands Management, and other agencies often assist CDFW with surveys of other habitats. Center for Natural Lands Management is leading efforts to restore a pond at Coachella Valley Preserve, while CDFW and BLM are restoring the barn pond at Dos Palmas Preserve. CDFW staff has been seeking Section 6 funding to improve existing refuges, and also is drafting a management plan to provide guidance for the management of all desert pupfish refuges. Additionally, CDFW staff is working with staff from other agencies to develop studies important for the future management of desert pupfish populations. CDFW staff has started implementing genetic protocols recommended by a pupfish geneticist; these protocols include inoculating existing desert pupfish populations with pupfish taken from a variety of habitats.

In 2010, CDFW and other agencies, including Imperial Irrigation District, Bureau of Reclamation, and U.S. Fish and Wildlife salvaged over one million desert pupfish from experimental ponds that were being dewatered after the federal landowner ran out of funds to maintain those ponds. Most of the salvaged fish were moved to permanent waters that already contained populations of the species and some were used to inoculate refuge populations.

Also in 2010, CDFW worked with staff from Orange County Vector Control District (OCVCD) and The Living Desert (TLD) to move 8,000 desert pupfish from a pond at OCVCD to two new ponds at TLD. Later that same year, CDFW moved 40 pupfish from one of the new ponds at TLD to a new pond at UCR Palm Desert campus. pupfish will be stocked in this pond in 2012. In 2011, 256 pupfish were introduced to the middle S pond at Dos Palmas, and there are plans to introduce pupfish into the upper S pond in the summer of 2012. At least three additional refuges are currently being planned, with several additional ones being considered.

Status in 2012

Pupfish populations appear to be stable or increasing in natural populations and generally stable in refuges. This assessment is based on monitoring surveys CDFW has conducted annually (at a minimum) since 2006 and in some cases since the mid 1990s. While extirpations of pupfish have occurred at some refuges, pupfish have been introduced into additional artificial habitats.