Mimosa bimucronata (Candolle) O. Kuntze, native to the American tropics, is the worst invasive tree species in China, where it is distributed in the southern coastal areas of Guangdong and Fujian provinces. It is characterized by rapid growth and waterlogging resistance, and was introduced in China for slope and bank protection. However, there is still a lack of effective molecular markers for its invasion management. In this study, we used a qubit dsDNA HS assay kit to extract DNA, and DNBSEQ-500 whole genome re-sequencing technology to obtain single nucleotide polymorphism (SNP) markers. In total, we developed and characterized 165 SNP markers. Observed (H_O) and expected heterozygosity (H_E) ranged from 0.0667 to 0.1000 and 0.1800 to 0.5000, respectively. The polymorphic information content (PIC) ranged from 0.1638 to 0.3750. These SNP markers will help to analyze the population genetic structure and manage M. bimucronata.