<p>Macadamia is a fruit tree with high economic value and high oil content, and is cultivated commercially in tropical and subtropical regions worldwide. Although the planting area of macadamia in China has ranked first in the world, research into the genetic diversity of available macadamia accessions in China is limited. The lack of core collection information hinders the efficient management and utilization of these accessions. This study is based on single nucleotide polymorphism (SNP) markers identified through whole-genome resequencing of 185 macadamia accessions from the USA, Australia, South Africa, Israel and China in our previous study. Following filtering, 6,266,537 high-quality SNP markers were used to investigate the genetic diversity of these accessions and to develop a core collection. Genetic diversity analysis revealed that these accessions exhibited low genetic diversity. Both phylogenetic and principal component analyses consistently divided these accessions into three groups according to species type: <i>Macadamia integrifolia</i>,<i> Macadamia tetraphylla</i> and their hybrids. Genetic differentiation index (<i>F</i>_<i>ST</i>) for the three groups ranged from 0.0147 to 0.1289, with <i>M. integrifolia</i> and <i>M. tetraphylla</i> groups exhibiting moderate genetic differentiation. Using Core Hunter II software, a core collection of 37 accessions representing 20% of the total accessions was developed. This core collection adequately represented the allelic richness and genetic diversity of the original population, consisting of 14 <i>M. tetraphylla</i> and 23 <i>M. integrifolia</i> accessions. Our results provide a rational and effective resource for future macadamia breeding and the conservation of genetic diversity in China.</p>