In recent years, South African conservation officials have noted the appearance of sarcoid tumour-like growths in Cape mountain zebra (Equus zebra zebra) populations. In domestic horses (Equus ferus caballus), a genetic predisposition for this bovine papillomavirusinduced tumour is reported. This investigation compared population genetic parameters within tumour-affected populations in Bontebok National Park and Gariep Dam Nature Reserve against Cape mountain zebra populations having few or no tumours in Karoo National Park and Karoo Nature Reserve in South Africa and Hartmann's mountain zebra populations from Namibia. Tumour-affected populations had the lowest levels of expected heterozygosity, gene diversity and polymorphism and highest values of internal relatedness and homozygosity by loci but not reaching levels of significance (P = 0.05). Wright's F_IS values indicated an overall deficit of heterozygotes in both affected and non-affected Cape mountain zebra populations. Considerable population substructuring, as indicated by FST values and Bayesian clustering, was revealed among all Cape mountain zebra populations. The results provide support for current conservation policies aimed at increasing levels of genetic diversity in isolated Cape mountain zebra populations.