BackgroundPueraria montanavar.lobata(kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships betweenPueraria montanavar.lobataand the other two varieties (P. montanavar.thomsoniiandP. montanavar.montana) remain debated. Although there is increasing evidence showing thatP. montanavar.lobataadapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes betweenP. montanavar.lobataand its closely related taxa.Results26 newly sequenced chloroplast genomes ofPuerariaaccessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties ofP. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes ofPuerariaand other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including sevenP. montanavar.lobata, 14P. montanavar.thomsoniiand sixP. montanavar.montana. Phylogenetic analysis revealed thatP. montanavar.lobataandP. montanavar.thomsoniiformed a clade, while all sampledP. montanavar.montanaformed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, andrps2) that account for among-site variation in selective constraint under the clade model between accessions of thePueraria montanavar.lobataclade and thePueraria montanavar.montanaclade.ConclusionOur data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining toP. montanavar.lobataand the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa ofP. montanacome from loci that own moderate variation and underwent modest selection.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09356-8.