Daniellia ogea and Daniellia oliveri are important tree species indigenous to Nigeria and have been used economically in various dimensions. To clearly understand their taxonomic affinity, there is need for characteristic evaluation at both morphological and molecular levels. Morphological characterization of the species has been done to some extent, but there is limited information on the molecular discrimination. This study was designed to assess the possibility of using DNA barcodes for taxonomic differentiation of the two tree species. Forty-Six (46) sequences representing three barcode loci (ITS, matK and trnL) were downloaded from the NCBI website, concatenated and evaluated using pairwise distance similarity, barcoding gap and tree-based method. The interspecific distance ranged from 1.2 (ITS) to 2.33 (ITS+trnL+matK) with the lowest average value of 0.05 (ITS) and the highest average value of 1.29 (ITS+trnL+matK). Among the concatenated barcode loci ITS+trnL+matK gave the highest species identification rate of 93.47% while matK had the best identification rate (82.40%) among the single barcodes. It was recommended that the two species can be discriminated using the plastid region matK and its concatenation with other barcode loci.