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GENETIC MANAGEMENT GUIDELINES

Mountain Zebra Equus zebra

Within Equus zebra two subspecies are currently recognised (Equus zebra hartmannae: Hartmann’s mountain zebra, HMZ, and Equus zebra zebra: Cape mountain zebra, CMZ). They are primarily differentiated by their habitat and size, with CMZ being slightly smaller (Wilson & Reeder 2005). For permitting purposes in southern Africa, Namibia and South Africa currently utilise Equus zebra hartmannae and Equus zebra zebra, respectively. Early molecular investigations based on mitochondrial DNA were unable to detect any subspecific genetic structure, however, differentiation at the subspecific level was detected based on microsatellite data(Moodley & Harley 2005). These subspecies are therefore not considered Evolutionarily Significant Units (ESUs) but rather Genetic Management Units (GMUs). Figure 1 illustrates the geographic distribution of these GMUs. Within E. z. zebra, additional genetic structure has been identified corresponding to the individual reserves in which these animals are found (Mountain Zebra National Park, De Hoop Nature Reserve, Kammanassie Nature Reserve; e.g. Kotze et al. 2019), however, this differentiation is the result of recent anthropogenic (human-mediated) fragmentation and isolation before the 1950s from hunting and reduced habitat (converted to pasture for livestock; Millar, 1970).

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Figure 1: Natural distribution of mountain zebra (Equus zebra) in green shading. Genetic Management Units (GMUs) are indicated by different symbols. Each point represents a locality which has been sampled for genetic data and thus the GMU (symbol) designation of each locality is based on genetic data. The inset indicates the part of Africa shown in the main map. Distribution data sources: South Africa – Birss, C., Rushworth, I., Collins, N. B., Peinke, D. & Buijs, D. 2017. Inferred natural distribution ranges of certain large mammals in South Africa. Unpublished GIS coverage. Namibia – Brown, C. J. (2005). Historic distribution of mammals in Namibia. Unpublished GIS coverage.

Management Level

Subspecies

Two subspecies of mountain zebra are recognised based on morphological characteristics (Wilson & Reeder 2005).

  • Equus zebra hartmannae (Hartmann’s mountain zebra, HMZ)
  • Equus zebra zebra (Cape mountain zebra, CMZ)


The guidelines provided in this document are based on genetic data translated into the Evolutionarily Significant Units (ESUs) and Genetic Management Units (GMUs) listed below. However, the name that is used for permits in southern Africa reflect the subspecies designations.

Evolutionarily Significant Units (ESUs)

No ESUs are recognised at present.

Genetic Management Units (GMUs)

There are two GMUs within the species corresponding to the two subspecies.

  • South-West (SW) (HMZ, E. z. hartmannae)
  • Southern (SO) (CMZ, E. z. zebra)

Management Boundaries

See Figure 1 for visual representation. Text descriptions follow.

Genetic Management Units (GMUs)

Genetic Management Units (GMUs)

  • South-West (SW): along the entire escarpment of Namibia, with a small number of individuals in south-west Angola.
  • Southern (SO): southern South Africa.

Genetic Risk

  • Global Nc: 37,017 (de Villiers et al. 2025; Patel et al. 2025)
  • South African Nc: 2,852-3,889 (de Villiers et al. 2025) 
  • Genetic indicators are calculated at GMU level. This is based on a best case scenario where gene flow is maintained.
  • If values are reported as a range, the average is used for subsequent calculations.
 

Table 1. Effective population size, Ne500 indicator, and confidence in the values calculated per ESU for mountain zebra. The colour of the GMU label is linked to the colour used in Figure 1. Colour of Ne500 and confidence text corresponds to positive (green) or negative  interpretation (orange/red). Overall Ne500 indicates the proportion of the total GMUs that have an Ne over 500.

Population genetic indicators
  • Ne500 indicator1:
    • South-West (SW) Nc: 33,666. Using an Nc:Ne ratio of 0.1-0.3, Ne = 3,367-10,100 (Patel et al. 2025).
    • Southern (SO) Nc: 2,852-3,889. Using an Nc:Ne ratio of 0.1-0.3, Ne = 337-1,011 (de Villiers et al. 2025).

Both management units have an Ne above 500 which indicates each GMU will maintain genetic diversity, assuming gene flow is maintained within GMUs, thus indicating lower genetic risk. *Although Ne based on census size is above 500, genetic data indicate that Ne for the largest subpopulation (Mountain Zebra National Park) is well below 500.

  • Proportion of populations maintained (PM2):
    • Global populations of mountain zebra comprise 2 GMUs (de Villiers et al. 2025; Patel et al. 2025), therefore the proportion of populations maintained globally: 2/2 = 1.
Diversity Loss
  • Functional variation: There is risk of functional variation loss, particularly in E. z. zebra, due to massive reduction in historical range causing fragmented/isolated populations with little potential for natural gene flow. This leaves CMZ at risk of genetic drift and inbreeding. Due to this, there has likely been a loss of traits that were adapted to habitats the species formerly occupied. 
  • Divergent lineages: There is risk of losing divergent lineages due to small remaining population sizes in several areas of its range. Genetic divergence among the relic subpopulations of E. z. zebra is primarily due to the high degree of anthropogenic isolation. Low levels of genetic diversity have made many populations increasingly vulnerable to disease, with outbreaks of sarcoid tumours becoming more common within inbred populations (e.g., Marais 2007).
Hybridisation/introgression
  • Cape mountain zebra and Hartmann’s mountain zebra are known to hybridise, with 28% of the CMZ population currently thought to be at risk (Hrabar et al. 2015).
  • There is some evidence of hybridisation between Cape mountain zebra (E. z.  zebra) and plains zebra (Equus quagga burchelli). No introgression has been seen as it is likely offspring between the two species are infertile (Dalton et al. 2017).
Lower turnover/constraints on adaptive opportunities
  • Historical bottlenecks have led to a narrow gene pool for mountain zebra, constraining their adaptive potential. This is furthered by founder effects in subpopulations derived from these original bottlenecked populations. Studies have documented low heterozygosity within the species in comparison to other zebra and equine species (Kotze et al. 2019).
In situ genetic threat level
  • In situ risk (High) 

Mountain zebras are at risk of continued diversity loss through fragmented habitats and isolated populations. Low heterozygosity within remaining populations may pose future issue to the health of the species. The Cape mountain zebra exists in smaller numbers than Hartmann’s mountain zebra and are therefore more likely to experience constraint on their adaptive opportunities. There is also significant risk of hybridisation, which could further affect diversity loss in the form of divergent lineage and functional variation loss. For other threats, see the IUCN Red List, South African Red List (CMZ), and South African Red List (HMZ) .

  • Confidence in in situ threat level
    • Confidence score (High) 

Confidence levels are supported by data on heterozygosity from recent genomic studies using microsatellite markers (Kotze et al. 2019) and IUCN or regional assessment data from within the last decade (de Villiers et al. 2025; Gosling et al. 2019; Hrabar et al. 2015; Patel et al. 2025).

Ex situ representation
  • Hartmann’s mountain zebra exists in captive populations globally, with 226 individuals within 59 institutions, in 15 countries and five continents (Europe, Asia, Central America, North America, and Africa) (Langenhorst 2025).
  • Cape mountain zebra exists within six captive populations in South Africa, totalling 143 individuals (Hrabart et al. 2015).
  • Captive populations may contain both GMUs and other zebra species, potentially complicating the genetic integrity of some ex situ stocks.
Figure 2. Effective population size compared to confidence in the value. Colour and shape of points and labelling corresponds to the GMUs in Figure 1 and Table 1. Dashed lines divide the x axis into above and below Ne500, and the y axis into low and high confidence. GMUs in the low confidence quadrant should be further surveyed to increase confidence in the evaluation. Those with high confidence below Ne500 should have increased genetic management.

1Proportion of populations within species with an effective population size (Ne) greater than 500
(https://www.gbf-indicators.org/metadata/headline/A-4) 

2Proportion of populations maintained within species
(https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html)

Management Guidelines

General management guidelines
  • Translocations between the GMUs should be prevented to maintain genetic differentiation.
  • However, if the species or GMUs are in imminent risk of extinction (poor to low diversity metrics and heavy sex-biased populations resulting in increased inbreeding) then translocations between the GMUs should be permitted.

South-West (SW)

  • Natural gene flow within this GMU should be encouraged to maintain genetic diversity and ensure continued population growth, keeping Ne > 500.

Southern (SO)

    • Plains zebra (Equus burchelli) should be removed from areas containing Cape mountain zebra (E. z. zebra) to prevent hybridisation.
    • To prevent the further loss of genetic diversity and maintain an Ne > 500, more effort should be made to encourage translocations and breeding between sites (farms, reserves, etc.) of E. z. zebra, primarily between members of natural populations not derived from common relic populations (Mountain Zebra National Park, Gamkaberg Nature Reserve, Kammanassie Nature Reserve).
  • Maintaining differentiation between Mountain Zebra National Park, De Hoop Nature Reserve, Kammanassie Nature Reserve is ill advised (see background).

IUCN Status:

  • Global: Least concern (indicated below).
  • South Africa: Least concern. 

Limitations & Assumptions

  • Some level of hybridisation between E. z. zebra and E. quagga burchelli (Burchell’s zebra) has already occurred within small populations in proximity to plains zebra.
  • The bulk of newly established E. z. zebra subpopulations originate from only Mountain Zebra National Park. However, individuals from Gamkaberg Nature Reserve and Kammanassie Nature Reserve have rarely been used in establishing new subpopulations, as both have fewer than 50 individuals.
  • Translocation of individuals between the GMUs has already occurred, as well as from species outside of these GMUs.

Priority Research

  • Collect more genetic data from the isolated subpopulations of E. z. zebra within South Africa to develop a better understanding of the rate of loss of genetic diversity and causes for the decline in population growth.
  • Genetic data are also needed from gaps in the genetic sampling such as the north-western Cape, southern Namibia, Sperrgebiet, Fish River area and south-west Angola.
  • Genome research is needed to better understand the evolutionary history and possible unique adaptations of the two mountain zebra GMUs.
  • More research is needed to evaluate the extent and effect of hybridisation within the different zebra species.
  • It is recommended that genetic monitoring studies be undertaken every 3-5 generations, if possible, to evaluate whether any changes in the genetic structure and diversity of this species have taken place, possibly warranting an update to these guidelines. Such studies would also contribute to the assessment of genetic indicators under the Kunming-Montreal Global Biodiversity Framework. Note: such studies would not be to assess local pedigree, but rather broad population structure and diversity, and hence the overall genetic health of the species.
  • Encourage authorities to collect genetic samples opportunistically for downstream genetic monitoring. This is essential for tracking the introduction or mixing of alleles when members of different relic stocks are used to seed new populations.

Cited References

  • Dalton, D.L., Zimmermann, D., Mnisi, C., Taplin, M., Novellie, P., Hrabar, H. and Kotze, A. 2017. Hiding in plain sight:evidence of hybridization between Cape mountainzebra (Equus zebrazebra) and plains zebra(Equus quagga burchelli). African Journal of Wildlife Research 47(1): 59–64 .http://dx.doi.org/10.3957/056.047.0059 
  • de Villiers, M.S., Kerley, G., and da Silva, J.M. 2025. A conservation assessment of Equus zebra ssp zebra. In Patel T, Smith C, Roxburgh L, da Silva JM & Raimondo D, editors. The Red List of Mammals of South Africa, Eswatini and Lesotho. South African National Biodiversity Institute and Endangered Wildlife Trust, South Africa.
  • Gosling, L.M., Muntifering, J., Kolberg, H., Uiseb, K. and King, S.R.B. 2019. Equus zebra (amended version of 2019 assessment). The IUCN Red List of Threatened Species 2019: e.T7960A160755590. https://dx.doi.org/10.2305/IUCN.UK.2019-1. Accessed on 28 November 2025.
  • Hrabar, H. & Kerley, G. I. H. (2013). Conservation goals for the Cape mountain zebra Equus zebra zebra – security in numbers? Oryx, 47(3), 403-409. doi.org/10.1017/S0030605311002018.
  • Kotzé, A. et al. (2019). Lessons for conservation management: monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra). PLoS ONE 14(7), e0220331.doi.org/10.1371/journal.pone.0220331.
  • Moodley, Y. & Harley, E. H. (2005). Population structuring in mountain zebras (Equus zebra): the molecular consequences of divergent demographic histories, Conservation Genetics, 6(6), 953-968. doi.org/10.1007/s10592-005-9083-8.
  • Patel, T., Roxburgh, L. and da Silva, J.M. 2025. A conservation assessment of Equus zebra ssp hartmannae. In Patel T, Smith C, Roxburgh L, da Silva JM & Raimondo D, editors. The Red List of Mammals of South Africa, Eswatini and Lesotho. South African National Biodiversity Institute and Endangered Wildlife Trust, South Africa.
  • Smith, R. K. et al. (2008). Monitoring and management of the endangered Cape mountain zebra Equus zebra zebra in the Western Cape, South Africa, African Journal of Ecology, 46(2), 207-213. doi.org/10.1111/j.1365-2028.2007.00893.x.
  • Sergio Solari, Robert J. Baker (2007). Mammal Species of the World: A Taxonomic and Geographic Reference by D. E. Wilson; D. M. Reeder, Journal of Mammalogy, 88(3), 824–830, doi.org/10.1644/06-MAMM-R-422.1.
  • Langenhorst, T. (2025): International studbook for Hartmann’s mountain zebra Equus zebra hartmannae 2024, current until 31.12.2024. Marwell Wildlife, UK.

Additional References

  • Marais, H. J. et al. (2007). Prevalence and body distribution of sarcoids in South African Cape mountain zebra (Equus zebra zebra). Journal of the South African Veterinary Association  78(3), 145-148. doi.org/10.4102/jsava.v78i3.306.

Consultation

  • IUCN SSC Conservation Genetics Specialist Group
  • IUCN SSC Equid Specialist Group

Acknowledgements

We are grateful to Drs Rae Smith and Peter Novellie for their valuable comments and for taking the necessary time and effort to critically review the initial guidelines.

Queries

If you have any additional questions related to these guidelines, please contact ConGen Africa at info@congenafrica.com.

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