Nile crocodile – ConGen Africa

GENETIC MANAGEMENT GUIDELINES

Nile crocodile Crocodylus niloticus

Within Africa, the Nile crocodile Crocodylus niloticus (Laurenti 1768), is one of five currently recognised crocodilian species. The species is found in 26 countries, from Egypt down to South Africa (Iseburg et al. 2019). The Nile crocodile was previously considered a single species but recent studies have clarified there are 2 distinct lineages: the Nile crocodile (C. niloticus) and the African crocodile (C. suchus), found in West and Central Africa. This distinction was made through phylogenetic analysis of mitochondrial and nuclear markers (Cunningham et al. 2016; Hekkala et al. 2011). For permitting purposes, Crocodylus niloticus is used across the entirety of its range. There are no currently recognised subspecies since C. suchus has been elevated to species level. There is evidence of biogeographical structuring based on mitochondrial DNA and microsatellite data within C. niloticus following the major river basins across northern, eastern, and southern Africa (van Asch et al. 2019; Versfeld 2016). This assessment used genetic evidence as the basis for naming two Evolutionarily Significant Units (ESUs) within Africa, and assigning eight Genetic Management Units (GMUs) within those. Figure 1 visualises these ESUs and GMUs across Africa.

Figure 1: Natural distributions of Nile crocodiles in Africa. Current distribution and its management units are indicated by coloured regions. Points represent a locality which has been sampled for genetic data and correspond through colour to the ESU they are within. The shape of these points indicates different management units within an ESU and are based on genetic data. ESU ranges are based on genetic data of populations. Distribution data source: Isberg, S., Combrink, X., Lippai, C. and Balaguera-Reina, S.A. 2019. Crocodylus niloticus. The IUCN Red List of Threatened Species 2019:e.T45433088A3010181. https://dx.doi.org/10.2305/IUCN.UK.2019-1.RLTS.T45433088A3010181.en [Accessed 14th November 2025]. Point data source: van Asch, B. et al. 2019. Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution. PLoS ONE, 14. https://doi.org/10.1371/journal.pone.0226505.

Management Level

Subspecies

There are no current subspecies identified currently for nile crocodiles.

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.

Evolutionarily Significant Units (ESUs)

North-eastern (NE)
Southern (SO)

Genetic Management Units (GMUs)

North-eastern (NE)
- Central-eastern (CEA) (Tana river system)
- Central (CE) (Semliki, Victoria Nile, and Albert Nile river systems)
- North-Nile (NN) (Lake Nasser and lower Nile river system)

Southern (SO)

- South-western (SW) (Kunene river system)
- South-central (CS) (Okovango river and lower Zambezi river systems)
- Eastern (EE) (Lake Nyassa and upper Zambezi river system)
- South-eastern (SE) (Limpopo river system)
- KwaZulu-Natal (KZN) (Coastal wetlands and estuaries)

Management boundaries

See Figure 1 for visual representation and figure legend for more detail.

Genetic Management Units (GMUs) Based on genetic data from van Asch et al. (2019), Versfeld (2016))

Southern (SO):

- South-west (SW): Namibia and Angola (Also potentially Gabon, Cameroon, and Equatorial Guinea).
- South-central (SC): Okavango Delta, Botswana, upstream or adjacent populations in central Zimbabwe.
- South-east (SE): Limpopo river system including adjacent populations in South Africa, central Mozambique, southern Zimbabwe.
- Eastern (EE): Lower shire in Southern Malawi (Lake Nyasa), southern Mozambique, Tanzania, southern Zambia, northern Zimbabwe, Rwanda, Madagascar.
- KwaZulu-Natal (KZN): KwaZulu-Natal coastal wetlands and estuaries, South Africa.

North-eastern (NE):
- Central-eastern (CEA): Kenya
- Central (CE): Uganda
- North-Nile (NN): Egypt
- Unknown: Sudan, South Sudan, Somalia.

Genetic Risk

Global Nc: 50,000-60,000 (Isburg et al. 2019)
South African Nc: 4,000 (Isberg et al. 2019)
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 median is used for subsequent calculations.

Table 1. Effective population size, Ne500 indicator, and confidence in the values calculated per GMU for Nile crocodile. 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.

Genetic Indicators

Ne500 indicator¹
- South-west (SW) Ne was based on genetic data from van Asch et al. 2019. For comparative context, Nc: 567 (Lyet et al. 2016).
- South-central (SC) Ne was based on genetic data from van Asch et al. 2019. For comparative context, Nc: 582-698 (Combrink et al. 2019).
- South-east (SE) Ne was based on genetic data from van Asch et al. 2019. For comparative context, Nc: 3,904 (Combrink et al. 2019).
- Eastern (EE) Ne was based on genetic data from van Asch et al. 2019. For comparative context, Nc: 10,270-17,614 Combrink et al. 2019).
- KwaZulu-Natal (KZN) Ne was based on genetic data from van Asch et al. 2019. For comparative context, individuals: 1,512. With assumed maturity percentage of 41 % specifically in this GMU (Combrink et al. 2019), Nc: 620.
- Central-eastern (CEA): There has been no genetic Ne calculated, but based on census size, its likely > 500. Information is only available Kenya and other localities within the north-eastern ESU where this GMU may be present are unknown. From Kenya alone, Nc: > 4,000 (Combrink et al. 2019). Using an Nc:Ne ratio of 0.1-0.3, Ne = 400-1,200. Based on this, it can be assumed the Ne for the whole GMU is above 500.
- Central (CE): There is limited information on the number of Nile crocodiles in Uganda where this GMU is identified. Other localities within the north-eastern ESU where this GMU may be present are unknown and therefore Ne500 cannot be calculated.
- North-Nile (NN) There has been no genetic Ne calculated, but based on census size, Nc: 3,000-4,000 (Combrink et al. 2019). Using an Nc:Ne ratio of 0.1-0.3, Ne = 350-1,050.

Based on Ne500, the GMUs within the southern ESU are most at risk. GMUs with Ne < 500 are highly susceptible to rapid loss of genetic diversity and are at high risk of extinction due to genetic threats. The north-eastern GMUs are understudied and more information is needed both on their genetics and numbers to be able to confidently calculate Ne500 either through genetic data or census size. Figure 2 summarises findings.

PM indicator ²:
- Global populations of Nile crocodile comprise 8 GMUs across 2 ESUs (van Asch et al. 2019), therefore the proportion of populations maintained globally: 8/8 = 1

Diversity Loss

Functional variation: There is risk of functional variation loss due to human interference in river systems causing fragmented/isolated populations, as well as overall small sub-population numbers in areas of its range. Other anthropogenic activity such as overexploitation through hunting for skin and human-crocodile conflict poses a threat to population numbers (Combrink et al. 2019). 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.

Hybridisation/introgression

There is substantial risk of introgression and hybridisation between the African crocodile (C. suchus) and the Nile crocodile (C. niloticus) due to them being considered the same species, with C. suchus as a subspecies of C. niloticus until 2011 (Hekkala et al. 2011). They had been managed as a singular species until that point. Presence of C. suchus individuals in the same gene pools as C. niloticus Has been identified within the central (CE) GMU (van Asch et al. 2019).
Breeding between ESUs is likely to occur at contact zones such as lake victoria. There is evidence of some breeding and introgression between GMUs within the southern ESU (van Asch et al. 2019).

Lower turnover/constraints on adaptive opportunities

Within Nile crocodiles, there has been a noted decline in effective population size, leading to reduced genetic diversity, inbreeding depression, and decreased ability to adapt to environmental change (Bishop et al. 2009).

In situ genetic threat level

In situ risk (Moderate)
Nile crocodiles are at risk of diversity loss through fractured habitats and isolated populations. Decline in effective population sizes within remaining populations may pose future risk. Several areas of the distribution are understudied and may be at risk. There is also significant risk to these subspecies of hybridisation with the African crocodile, which could further affect diversity loss in the form of divergent lineage and functional variation loss. The overall assessment of the species indicates that populations are stable (Iseburg et al. 2016). For more threats, see the IUCN Red List and South African Red List.

Confidence in in situ threat level

- Confidence score (Low)

Confidence levels are supported by data from recent genomic studies (van Asch et al. 2019; Versfeld 2016), IUCN data on populations from within the last decade (Iseburg et al. 2019), and conservation surveys (Combrink et al. 2019). Large portions of the range are still lacking data on population numbers of Nile crocodile (such as Sudan, South Sudan, and other areas of the northern distribution) and available information does not provide a full picture of their numbers for many areas due to the study and survey limitations (SW, SE, and SC GMUs).

Ex situ representation

Nile crocodiles exist in captive populations globally, with 4600 individuals held within 91 institutions across 35 countries (The majority within Europe, North America, and South Africa) (Iseburg et al. 2016)
Captive populations may contain multiple GMUs or ESUs with no distinction as well as other crocodile species, potentially complicating the genetics 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 GMU 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. ESUs 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. Note that the CEA and CE GMUs are not shown due to data deficiency.

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

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

Management Guidelines

No translocation between GMUs (defined by microsatellites) until further genetic information is provided, however natural migration and gene flow should not be hindered.
Captive bred individuals and those on private ranches must be genetically tested before translocation to ensure no admixture between GMUs, ESUs, or hybrid individuals.
If populations are at imminent risk of extinction, due to reduced effective population size or inbreeding, Translocation should be permitted between GMUs.

IUCN Status:

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

Limitations & Assumptions

River basins in central and northern Africa remain under-sampled or simply not sampled at all and data from these areas may change ESUs or GMUs currently proposed.
Genetic data that is available is based on small sample sizes.
Private ranches in South Africa may have some individuals from other GMUs found in more northern populations such as those in the Zambezi or Okavango rivers.
Translocation of individuals from different GMUs and from the once considered subspecies, C. suchus, has already occurred.

Priority Research

Additional samples from both ESUs should be assessed to help clarify if the suggested GMUs and ESUs should be considered distinct. Current proposed separation is precautionary until further testing can be done.
Surveys in areas currently lacking census data (primarily central and east Africa), as well as more comprehensive surveys across the species’ distribution.
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.

Cited References

Bishop, J. M., Leslie, A. J., Bourquin, S. L. and O’Ryan, C. 2009. Reduced effective population size in an overexploited population of the Nile crocodile (Crocodylus niloticus). Biological Conservation, 142 (10), pp. 2335-2341. https://doi.org/10.1016/j.biocon.2009.05.016
Cunningham, S., Shirley, M., and Hekkala, E., 2016. Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807). PeerJ, 4. https://doi.org/10.7717/peerj.1901
Combrink, X., Korrûbel, J.L., Taylor, R., Kyle, R. and Ross, P., 2011. Evidence of a declining Nile crocodile (Crocodylus niloticus) population at Lake Sibaya, South Africa. South African Journal of Wildlife Research, 41(2), pp.145-157.
Combrink, X., Lippai, C. and Fergusson, R. (2019). Nile Crocodile Crocodylus niloticus. In Crocodiles. Status Survey and Conservation Action Plan. Fourth Edition, ed. by S.C. Manolis and C. Stevenson. Crocodile Specialist Group: Darwin. 28pp.
Hekkala, E. et al. 2011. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile.. Molecular ecology, 20 20, pp. 4199-215 . https://doi.org/10.1111/j.1365-294X.2011.05245.x
Isberg, S., Combrink, X., Lippai, C. and Balaguera-Reina, S.A. 2019. Crocodylus niloticus. The IUCN Red List of Threatened Species 2019:e.T45433088A3010181. https://dx.doi.org/10.2305/IUCN.UK.2019-1.RLTS.T45433088A3010181.en
van Asch, B. et al. 2019. Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution. PLoS ONE, 14. https://doi.org/10.1371/journal.pone.0226505
Versfeld, W. F. 2016. Nile crocodile (Crocodylus niloticus) genetic diversity and population structure, within the lower Kunene and Okavango Rivers of northern Namibia. Msc Thesis. Stellenbosch University.

Additional References

Turner, A. and Marais, J. 2017. Crocodylus niloticus. Red List of South African Species. South African Biodiversity Institute.

Consultation

Acknowledgements

Queries

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