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Abstract Medicago truncatulais a model legume that has been extensively investigated in diverse subdisciplines of plant science.Medicago littoraliscan interbreed withM. truncatulaandM. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated thatM. truncatulaaccessions are heterogeneous but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverseM. truncatulaaccessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from bothM. truncatulaandM. littoralis.Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material.Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. TwoMedicagoaccessions were placed within aM. italicasubclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within theM. littoralissubclade. Our results suggest that theM. truncatulaaccession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.