South Africa is a leading producer of macadamia nuts worldwide, but, to compete globally the industry needs to invest in breeding programmes to develop new cultivars and improve existing breeding material. However, a better understanding of the genetic diversity and genomic architecture of macadamia cultivars in South Africa is first required in order to leverage new genomics technologies and phenotypic data for macadamia improvement. Furthermore, the South African macadamia industry would benefit greatly from DNA marker technologies to better understand the genetic diversity amongst and within commonly planted cultivars, and for future orchard design to maximize the advantageous effects of outcrossing on nut yield and quality. We are contributing to this through a project funded by Macadamias South Africa (SAMAC) to sequence the genomes of some key cultivars in South Africa and develop a microsatellite marker tool for routine screening of existing material planted in orchards and newly propagated material from commercial nurseries.