Understanding the genetic diversity of Acacia melanoxylon is very important in species selection and improvement. The present study aimed to identify microsatellite markers and determine the genetic diversity of 45 preferred clones selected from 9 Chinese districts. Seventy-six simple sequence repeat (SSR) markers developed for other Acacia species were screened. Seventeen SSR markers showed polymorphic patterns and amplified 134 alleles. Polymorphism information content (PIC) values ranged from 0.044 to 0.911. The average allele number per locus ranged between 2 and 18, averaging 8.06. Nine SSR markers were highly informative, with PIC values above 0.60. These findings demonstrated that SSR markers could be used to differentiate A. melanoxylon genotypes. Cluster analysis using UPGMA separated the 45 clones into 3 distinct groups at a similarity coefficient of 0.72. The clone groups identified in this study would be useful in developing intraspecific hybrids to exploit hybrid vigor as well as for commercial cultivation and genetic base broadening. The DNA fingerprints obtained for each clone could be used for biodiversity conservation.
