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Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more diverse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) <i>Macadamia integrifolia</i>, (ii) <i>M. tetraphylla</i>, and (iii) <i>M. jansenii</i> and <i>M. ternifolia</i>, and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one <i>M. integrifolia</i> and four <i>M. tetraphylla</i> accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure examples of one of the four species and 15 as hybrids of <i>M. integrifolia</i> and <i>M. tetraphylla</i>. The admixed accessions showed the highest genetic diversity followed by <i>M. integrifolia</i>, while <i>M. ternifolia</i> and <i>M. jansenii</i> accessions were the least diverse. Mantel test analysis showed a significant correlation between genetic and geographic distance for <i>M. integrifolia</i> (r = 0.51, <i>p</i> = 0.05) and a positive but not significant correlation for <i>M. tetraphylla</i> (r = 0.45, <i>p</i> = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.