Analyses of nuclear ribosomal DNA have suggested the paraphyly of Syringa with respect to Ligustrum, a hypothesis requiring further testing from other sources of data. In addition, relationships among lineages of Syringa have not been resolved. In this study, we used DNA sequences of two nuclear and five plastid regions to better resolve phylogenetic relationships of Syringa and Ligustrum. Our results support the derivation of Ligustrum from within Syringa, thus the paraphyly of Syringa. Six series are recognized in Syringa and their relationships are: (Syringa, (Pinnatifoliae, (Ligustrae, (Ligustrina, (Pubescentes, Villosae))))). Subgenus Syringa as traditionally defined is paraphyletic, containing subgenus Ligustrina. The Syringa pubescens complex may be paraphyletic with S. pubescens more closely related to the Syringa pinetorum complex than to other species of its own complex. Our estimated times of divergence suggest that series of Syringa have diversified in the middle Miocene (9.65–17.67 mya), each with unique morphology.