We present a molecular analysis to determine whether Eugenia boerlagei Merr. (Myrtaceae) is to be included in Eugenia or Syzygium based on sequences of cpDNA fragments namely atpB-rbcL intergenic spacer. In this study we used seven specimens of Syzygium sect. Jambosa, three of Syzygium sect. Syzygium, two of Eugenia s.s. and one of Eugenia boerlagei Merr. and Baeckea ovalifolia and B. tuberculata as the outgroup. The results showed that Eugenia boerlagei is better placed in Syzygium.