Abstract: Based on Sequences analysis of ITS-rpl16, the taxon relationships among the existing 14 species of the genus Acacia s.l. in China were examined. All the species tested were clustered into three categories. Three species native to China falled into one clade, indicating that A. instica and A. pennata are closely related and from a sister group together with A. catehu. Based on sequences analysis of matK, the taxon relationships among 40 species of the genus Acacia and 1 outgroup species were examined, indicating that: 1.The subgenera Acacia and Phyllodineae are monophyletic, while the Subg. Aculeiferum is polyphyletic. 2.The species native to China were clustered together with the African species, indicating closer relationships among them.