Macadamias (Macadamia integrifolia, M. tetraphylla, and their hybrids) are native to the east coast of Australia, and are grown commercially around the world for their high quality edible nut kernel. Breeding new cultivars for high nut yield is a lengthy and laborious process that can take over two decades. Evaluations are time-consuming due to the long juvenile period of four or more years, and the low correlation between young and mature tree yield means that at least eight years of evaluations are required. Furthermore, yield has low heritability, and the large tree size necessitates low field planting density, and thus increases land use and evaluation costs. It is hypothesised that genetic gain for yield may be increased, compared to traditional breeding approaches, through the use of strategies including (i) indirect selection using yield component traits, (ii) marker-assisted selection and (iii) genomic selection. This thesis employed an experimental population of 295 seedling progeny and their 29 parents, at four sites across southeast Queensland, that were genotyped for 4,113 SNPs and 16,171 silicoDArT markers detected using Diversity Arrays Technology (DArT) methods. Population structure, genetic diversity and linkage disequilibrium (LD) between SNP markers was quantified to inform subsequent genomics analysis. LD decay was initially rapid at short distances (r 2 = 0.124 for SNPs within 1 kb of each other), but low level LD persisted for long distances. The seedling population was relatively genetically diverse (HE = 0.255), and very similar in diversity to that of the 29 parents (0.250). Furthermore, progeny with M. integrifolia x M. tetraphylla ancestry were more genetically diverse (HE = 0.278) than M. integrifolia seedlings (HE = 0.189). Progeny were moderately differentiated and clustered into three distinct groups, which represented M. integrifolia germplasm and two hybrid groups. Flowering and nut characteristics, tree growth and yield were measured on each tree. Estimations of trait heritability and genetic correlations between each component trait and yield were used to calculate selection efficiency of indirectly selecting for yield using component traits. Kernel recovery, an economically important trait, had high heritability (h 2 = 0.76) but was negatively genetically correlated with yield (rg =-0.27). Trunk circumference correlated strongly with yield (rg = 0.72) and was moderately heritable (h 2 = 0.44); however, a breeding aim is to reduce tree size without compromising yield. No component traits were appropriate or effective for indirectly selecting for high yield.