Research efforts to increase the agricultural sustainability productivity of minor crops, particularly underutilized legumes are strategic approaches to mitigating the risks of total reliance on a few major crops. Integrating these legumes into broader genetic frameworks alongside major crop counterparts is imperative, utilizing recommended DNA barcoding methodologies. This study uses DNA barcoding techniques to undertake the phylogenetic analysis of 16 Fabaceae family species. The efficacy of core barcoding chloroplast markers, rbcL, and matK, for species classification, was also evaluated. To validate the findings from this study, phylogenetic analysis of complete chloroplast genomes from 11 species was employed, providing robust confirmation of the classification methodology. The amino acid sequences of the rbcL and matK genes from 15 species were retrieved from the NCBI database. In comparison, the rbcL and matK genes of one species (Macrotyloma geocarpum) were sequenced using the Sanger method. Raw nucleotide sequences were cleaned with BioEdit software, and contig sequences were generated using Codon code Aligner software. Subsequently, these sequences were translated into amino acid sequences via ExpaSy translator. Alignment was performed using the MUSCLE algorithm within the MEGA 11 program. Phylogenetic trees were constructed using neighbor-joining, maximum likelihood, and maximum parsimony algorithms. The double barcodes (matK + rbcL) and single barcode (rbcL) classified the selected legumes randomly; however, the matK gene classified the legumes down to the genus and species levels. It also revealed that Cajanus cajan, an underutilized legume, is the closest to Vigna unguiculata, implying the possibility of genetically improving C. cajan using the V. unguiculata genome. The matK gene also gave a similar result to that of the chloroplast genome. Consequently, the matK gene is recommended as a core barcode sequence in the Fabaceae family.