Background:In theSesamumspecies complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships.Results:In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum,Sesamum angolense,Sesamum pedaloides,Ceratotheca sesamoides(syn.Sesamum sesamoides),Ceratotheca triloba(syn.Sesamum trilobum), andSesamum radiatum) and a Korean cultivar,Sesamum indicumcv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863–153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, includingndhA,ndhE,ndhF,ycf1, andpsaC–ndhD. Concordant tree topologies suggestndhFas a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate thatS. radiatum(2n = 64) occurred concomitantly with the sister speciesC. sesamoides(2n = 32) approximately 0.05 million years ago (Mya). In addition,S. alatumwas clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others.Conclusion:Altogether, we propose to renameC. sesamoidesandC. trilobaasS. sesamoidesandS. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in theSesamumspecies complex.