Two subspecies are universally accepted: Kinosternon sonoriense sonoriense (LeConte, 1854) and K. s. longifemorale Iverson, 1981 (Smith and Smith 1980, Iverson 1981, Fritz and Havaš 2007, TTWG 2021). Hurtado-Gómez et al. (2024) analyzed phylogeographic structure and taxonomic limits within the genus Kinosternon that demonstrated deep intrageneric divergences; they proposed the recognition of three subgenera: Kinosternon, Cryptochelys, and Thyrosternum. The subgenus Kinosternon was found to include K. abaxillare, K. acutum, K. chimalhuaca, K. cora, K. creaseri, K. herrerai, K. hirtipes, K. integrum, K. oaxacae, K. sonoriense, K. vogti, and K. scorpioides with its three subspecies, K. s. scorpioides, K. s. albogulare, and K. s. cruentatum, with the latter two recognized as probable separate species. Kinosternon alamosae was later assigned to the same subgenus based on morphology (J.B. Iverson, unpubl. data). TTWG (in press) agrees with this proposed taxonomy.

The Sonora Mud Turtle, Kinosternon sonoriense, remains common in parts of its geographic range, occurring in stable populations at high population densities despite adverse environmental conditions. The species is not subject to targeted take and occurs in several protected areas. However, certain populations have disappeared (e.g., Colorado River), become critically endangered (e.g., the subspecies K. s. longifemorale), or remain unstudied (populations of K. s. sonoriense in Mexico). Kinosternon sonoriense remains common below the Mogollon Rim and in the Madrean Sky Islands, but faces the same threats that eliminated or endangered other populations – widespread groundwater extraction, impoundment failure, exotic species, and climate change.

The Sonoyta Mud Turtle (K. s. longifemorale), restricted to a small and heavily impacted area along the Mexico–USA border, was recently assessed as Critically Endangered on the IUCN Red List (Rosen and Stone 2017).

Kinosternon sonoriense was assessed in early 1996 as Least Concern (LC) by the IUCN Tortoise and Freshwater Turtle Specialist Group (TFTSG) (Behler 1996, TTWG 2021). However, around the same time, Baillie and Groombridge (1996) erroneously listed it as Vulnerable (VU A1c; criteria version 2.3, indicating a 20% population decline over three generations), citing the TFTSG as the source (but evidently sourced from before 1996, earlier than Behler's unpublished assessments). However, no formal 1996 Red List assessment of K. sonoriense was ever submitted by the TFTSG, and the VU listing was presumably weighted by the precarious status of the subspecies K. s. longifemorale. When the whole species was re-assessed in 2011, the typical subspecies K. s. sonoriense was found to be more widespread and locally abundant than previously assumed, and the species overall was assessed at that time as Near Threatened (NT) (van Dijk 2011). The species remains common in several locations; however, threats to aquatic habitats continue to increase, exacerbated by climate change and drought-induced desertification, making retention at NT inappropriate. It is therefore assessed as Vulnerable (VU) at this time under criterion A4c (version 3.1), indicating a ca ≥30% decline over the past two generations (24 years) and one generation projected into the future (12 years), due primarily to an ongoing decline in habitat quality.

Kinosternon sonoriense is native to the Gila River and endorheic drainages in the Madrean Sky Islands and below the Mogollon Rim in southeastern Arizona and southwestern New Mexico, the Lower Colorado basin of USA and Mexico, and Baja California and endorheic drainages of Sonora and Chihuahua (Iverson 1992, TTWG 2021, Stone et al. 2022). The species had an estimated historical indigenous range (area of occupancy, AOO) of 172,315 sq. km, and an estimated historical indigenous extent of occurrence (EOO) of 375,769 sq. km (TTWG in press). Both AOO and EOO have declined and are continuing to decline. Populations have been recorded at altitudes ranging from 300 to 2,100 m asl. An estimate of current AOO of K. sonoriense using a maximum entropy distribution model (MaxEnt) delineated a much larger potential AOO of 284,101 sq. km (Berriozabal-Islas et al. 2020), clearly at odds with the known distribution.

The subspecies K. s. sonoriense had an estimated historical indigenous range (AOO) of 170,611 sq. km (TTWG in press), including: the Gila, Lower Colorado, Bill Williams, and endorheic drainages in southern Arizona, southwestern New Mexico, and extreme southeastern California, USA, as well as the Magdalena, Sonora, upper Yaquia and upper Fuerte [Urique] drainages of Sonora and endorheic basins of western Chihuahua, Mexico (Iverson 1992, TTWG 2021, Stone et al. 2022). Kinosternon s. sonoriense is likely extirpated from California, Nevada, and Baja California in the Colorado River drainage and the Gila River drainage below Phoenix in western Arizona (Lovich and Beaman 2008, TTWG in press). The current extant range is ca 149,532 sq. km, an approximately 12.3% decline from the historical indigenous range, but the actual AOO is unclear, although certainly significantly smaller than either the indigenous or extant range.

The microendemic subspecies K. s. longifemorale had an estimated historical indigenous range (AOO) of 1,704 sq. km (TTWG 2021) and an original EOO of 2,295 sq. km in the Rio Sonoyta basin on the border of Arizona (USA) and Sonora (Mexico) (TTWG in press). Its current AOO and EOO are very much smaller, with the AOO currently estimated as less than 2 sq. km (Rosen and Stone 2017).

Aquatic habitats within the geographic range of K. sonoriense are typically isolated and small. As a result, the largest populations include fewer than 1,000 individuals, often occurring at high population densities (Stone et al. 2022). Stable populations occur in canyons that go dry in some years (Stone 2001, Hensley et al. 2010), and many populations are centred on impoundments constructed by humans to water livestock (Stone et al. 2022). No population data are available concerning Mexican populations (Rosen and Melendez 2010). Kinosternon s. sonoriense is likely extirpated in the Colorado River and Gila River below Phoenix, Arizona (Lovich and Beaman 2008). Two theses and a dissertation produced during 1974–1987 focused on demography in several populations in the Mogollon Rim region of Arizona (Hulse 1974a, Emslie 1982, Rosen 1987). The population at Montezuma Well National Monument has been intermittently monitored in recent years (Lovich et al. 2012), but otherwise populations near the Mogollon Rim have not been sampled recently (Stone et al. 2022). In the Madrean Sky Islands, several populations of K. s. sonoriense have been subjects of intensive (Stitt and Swann 2000) and long-term studies (van Loben Sels et al. 1997, Hall and Steidl 2007, Stone et al. 2015), with data spanning from the early 1990s until the present (Stone et al. 2022). Multiple populations have been documented from at least seven Sky Island ranges (Stone et al. 2022).

Kinosternon s. longifemorale is considered Endangered in both Mexico (SEMARNAT 2010) and USA (USFWS 2017a, 2017b), and Critically Endangered on the IUCN Red List (Rosen and Stone 2017). Five populations of K. s. longifemorale are known. The population at Quitobaquito Oasis (in Organ Pipe Cactus National Monument, Arizona) declined from several hundred in the late 1950s to about 100 in the early 1980s. Habitat improvements increased the population to about 130 turtles in the early 1990s, but further declines in water inflow soon occurred. Intensive maintenance and further renovations stabilized water levels, and the population rebounded again (USFWS 2017a). However, construction of the USA–Mexico border wall correlated with further decreases in water levels and reduced spring discharge, prompting another round of aquatic habitat restoration, currently ongoing. In Mexico, the only large, reasonably secure population of K. s. longifemorale occurs at Papalote Reach, a spring-fed reach associated with the Río Sonoyta, within the Pinacate Biosphere Reserve. The reach was 1.5–3.0 km in length and perennial until the early 21st century, when prolonged drought and pumping of the aquifer rendered it intermittent (USFWS 2017a). However, despite reduced water levels, the population at Papalote Reach appears stable over the past 12 years with population estimates of 268–351 turtles (Grageda Garcia and Garcia Miranda 2018, Grageda Garcia and Bogan 2019); making it the largest population of K. s. longifemorale known. Two other small populations from the Rio Sonoyta are associated with semi-permanent pools resulting from artificial dams and waste water effluent in the town of Sonoyta. A fifth population, possibly introduced, occurs farther south near the city of Quitovac (Rosen et al. 2010).

Kinosternon sonoriense occurs in a wide variety of permanent (rarely or never dries), intermittent (dries annually or during drought), and ephemeral (temporary) aquatic habitats (Rosen 1987, van Loben Sels et al. 1997, Stone 2001, Stone et al. 2022). Populations occur in both lotic and lentic habitats. Populations around the Mogollon Rim are usually in permanent aquatic habitats at relatively low elevations (404–1,219 m asl.; Hulse 1974a, Emslie 1982, Rosen 1987). Populations in the Madrean Sky Islands occur at intermediate elevations (828–1,762 m) and are typically centred on permanent or intermittent impoundments built by humans to water livestock (van Loben Sels et al. 1997, Stone et al. 2015), though undammed intermittent streams also harbour populations (Stitt and Swann 2000, Hall and Steidl 2007). In one Sky Island, intermittent impoundments connected to canyon reaches with ephemeral pools harboured the largest populations (Stanila 2009, Stone et al. 2015). Although fewer data are available, K. s. sonoriense appears to be mostly montane in its southern range and is found at elevations up to 2100 m in Mexico (Rosen and Melendez 2010, Legler and Vogt 2013). Populations of K. s. longifemorale occur in isolated wetlands at low elevations (300–425 m; USFWS 2017b).

Kinosternon sonoriense uses terrestrial habitat in a variety of contexts, including estivating on land during drought  (Ligon and Stone 2003), making seasonal movements between permanent and ephemeral aquatic habitats (Stone et al. 2015), undergoing terrestrial flight responses when disturbed in shallow water (Stone et al. 2011), and long-distance dispersal within and among drainages (Stone et al. 2015).

Kinosternon sonoriense is preferentially carnivorous, including plant matter in its diet when the availability of animal food is limited (Hulse 1974b). Typical prey includes benthic insects, snails and small crustaceans (Hulse 1974b), though vertebrates are sometimes eaten as carrion or prey (Stone et al. 2022). Maximum straight-length carapace length (SCL) for K. s. sonoriense is 17.5 cm for females (Rosen 1987) and 16.8 cm for males (van Loben Sels et al. 1997); maximum SCL for K. s. longifemorale is 14.8 cm for females and 13.7 cm SCL for males (Rosen and Stone 2017). There is considerable geographic variation in body size, with mean female SCL ranging between 11.2–14.5 cm among populations (Rosen 1987). Hatchlings may be as small as 22.3 mm SCL (Iverson 1991) and weigh 1–3 g (van Loben Sels et al. 1997). Minimum size at sexual maturity for females was 9.0–12.5 cm SCL (Hulse 1974a, 1982; van Loben Sels et al. 1997; Lovich et al. 2012), and estimated ages at maturity varied from 5–9 yrs (Rosen 1987, Hulse 1974a), with generation time estimated as 12 yrs (Rosen and Lowe 1996, Iverson, 2024). At lower elevations, immature males grow rapidly and matured at 5–6 yrs and 7.6–8.2 cm SCL, whereas growth was slower at higher elevations and males matured at 7–8 yrs and 9.1–9.8 cm SCL (Hulse 1982). Mean clutch size among populations varies from 3.1–8.1 eggs, with a range of 1–12 eggs (Stone et al. 2022). Repeated X-rays of individual females indicate annual clutch frequencies of 0–3 clutches per year in multiple populations (van Loben Sels et al. 1997, Lovich et al. 2012). Longevity may exceed 45 years in captivity and the wild (Slavens and Slavens 2000, Stone et al. 2022).

Kinosternon sonoriense is threatened by habitat loss, habitat fragmentation, exotic species, and climate change. Irrigation, water diversion, and groundwater pumping reduce groundwater and surface water availability and alter riparian vegetation, especially impacting populations of K. s. longifemorale and populations of K. s. sonoriense in the Colorado and Gila rivers. The construction of large dams in the Colorado and Gila drainages have de-watered large sections of former river channel while turning other sections into large reservoirs that are generally unsuitable for mud turtles (Stone et al. 2022). Perennial streams at lower elevations maintain connectivity among montane canyons; therefore, habitat loss at lower elevations creates habitat fragmentation and isolation of populations at higher elevations (Hall and Steidl 2007).  

At higher elevation sites, most known populations of K. sonoriense occur in anthropogenic impoundments. Siltation and dam failures at small dams negatively impact populations of both subspecies. In one range, 15 of 21 impoundments had structural or siltation problems, including nine that were permanently dry (Stone et al. 2015, 2022). Impoundment failure directly impacts local populations but also fragments the habitat and decreases connectivity, likely isolating populations. 

Exotic crayfish, bullfrogs, and predatory fishes have all been implicated in negative impacts on K. sonoriense populations. All the above threats to K. sonoriense populations are exacerbated by prolonged drought and increased temperatures, which are expected to persist and escalate due to climate change (Seager et al. 2013, IPCC 2021). According to a modelling study by Berriozabal-Islas et al. (2020), climate change may affect K. sonoriense, potentially leading to a reduction in its currently estimated potential AOO of 284,101 sq. km to 185,167 sq. km, signifying a decrease of up to ca 35% by 2070 in an extreme global warming modelling scenario such as RCP85 (Representative Concentration Pathway 8.5). Despite accelerating threats, impacts have not been assessed at most known localities, and the full geographic extent and intensity of threats are unknown. Therefore, the status of the species as a whole is somewhat unclear (Stone et al. 2022). Furthermore, monitoring and conservation efforts are complicated by narcotics smuggling and human trafficking in the area (van Dijk 2011).

Kinosternon sonoriense is in the pet trade in insignificant numbers, and has not been reported to be used for human consumption.

Kinosternon sonoriense is rated as a Species of Greatest Conservation Need in Arizona and New Mexico, and a Species of Special Concern in California (Stone et al. 2022). The species has been listed in CITES Appendix II as Kinosternon spp. as of 2023.

In the United States, K. sonoriense is restricted from exploitation in Arizona through area restrictions where collection is not permitted (including all protected areas). New Mexico has an annual bag limit of five K. sonoriense, whereas California has no collection restrictions. Turtles are protected from exploitation under Mexican wildlife and natural resource legislation, but implementation is uneven (van Dijk 2011).

Kinosternon s. longifemorale is considered Endangered in both Mexico (SEMARNAT 2010) and USA (USFWS 2017b), and Critically Endangered on the IUCN Red List (Rosen and Stone 2017). Critical habitat for the population at Quitobaquito Oasis was formally designated in 2020 (USFWS 2020) and a USFWS Recovery Plan is currently being drafted. Increased management actions at Quitobaquito Oasis and collaboration with Mexico to address habitat loss in the Río Sonoyta are expected.

Since 2007, the Arizona Game and Fish Department, National Park Service, and the Arizona-Sonora Desert Museum (ASDM) have maintained an assurance colony of K. s. longifemorale (Riedle et al. 2012, USFWS 2017a). Currently, the assurance colony at ASDM totals 28 turtles, and is doing well enough to consider adding additional assurance colonies at separate sites. Kinosternon sonoriense inhabits a number of protected areas in each country of occurrence, including Montezuma Well and Organ Pipe Cactus National Monuments in Arizona, Coronado National Forest in Arizona and New Mexico, and Reserva de la Biosfera El Pinacate y Gran Desierto de Altar in Mexico (Stone et al. 2022). However, the protected status of these areas does not safeguard the habitat or species from groundwater loss and climate change.

Actions that restore or augment surface flow are needed to provide aquatic habitat and maintain connectivity among populations (Hall and Steidl 2007, Stone et al. 2015). Additionally, Stone et al. (2014) proposed two measures: restoring impoundments by dam repair and silt removal to increase the number of populations; and building small trencheras (i.e., loose rock dams, Norman et al. 2016) in canyon beds to increase aquatic habitat in canyons that connect populations. Constructing additional small impoundments in canyons would be a cost-effective means of ensuring population persistence (Stone et al. 2022).

Range-wide population assessments, further natural history studies, and confirmation of the occurrence of secure populations in protected areas in Mexico would be desirable. Intensive efforts will be needed to safeguard and restore remaining habitat of K. s. longifemorale, both at the only site in the United States (State and partner efforts in place and ongoing) and in the Río Sonoyta in Mexico (cross-border partnership public-NGO developing in recent years).