The study reports the first DNA-barcode and molecular phylogeny of the East African endemic tree species Melia volkensii using the standard two-locus plant barcoding genes (rbcL and matK). The two genes were amplified and the PCR products sequenced. Complete coding sequences were obtained for both genes. The edited and aligned sequences had lengths of 1371 bp for rbcL and 1524 bp for matK. These DNA sequences were deposited into the DNA Data Bank of Japan (DDBJ) with cross-listing in the European Molecular Biology Labaratory (EMBL) and GenBank databases. The deposited gene sequences were then subjected to separate nucleotide BLASTs in NCBI's GenBank database. Out of 100 Blast results in which the query (M. volkensii) had 96-100 percentage similarity in nucleotide sequence for the rbcL gene and 90-100% similarity for the matK gene, only 16 taxa had data for both rbcL and matK genes. These 16 taxa were used for the phylogenetic analysis and comprised of 6, 9 and 1 taxa respectively from the families Meliaceae, Simaroubaceae and Rutaceae. The barcode allowed adequate discrimination of the taxa into their respective generic and species clades. Availability of a barcode for M. volkensii will ease identification of the species, provide more robust phylogenetic reconstructions and allow for better tracking of its exotic dispersal.