Toona ciliata var. pubescens is considered an endangered tree species native to China. In order to help develop a conservation program for this species, we evaluated its genetic diversity and population genetics. We isolated microsatellite DNA loci using streptavidin beads. A genomic library, enriched with microsatellites, was constructed and screened by sequencing. We detected 8 polymorphic microsatellite loci from the tree tissue samples. The population of T. ciliata var.