The South African Angora goat industry makes the largest contribution to global mohair production. Mohair is a luxury fibre and production of a high quality clip is essential. For many years genetic improvement of Angoras in South Africa was based on quantitative selection. Genome mapping efforts provided new avenues for improvement and a quantitative trait loci (QTL) study was initiated to identify QTL associated with mohair traits. The aim of this study was to describe the genetic diversity of the reference population using the available stud and commercial herds with full phenotypic records. The most appropriate QTL design was identified based on the population structure with regard to the families and number of bucks available for breeding. Four herds, consisting of 1067 pure bred goats in 12 half-sib families, were included. Blood samples were obtained from the herds, 94 markers were tested and diversity parameters were estimated. The average number of alleles per marker varied between 5.4 and 7.2 amongst the herds, whereas the observed heterozygosity varied between 0.59 and 0.67. The genetic structure of these herds was found appropriate for use as a reference population as they showed sufficient genetic variability.