Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To minePueraria montanachloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104P. montanaaccessions from across China.P. montana’s chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in theP. montanachloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported fourP. montanaclades.P. montanavariations were conserved among and within clades, which showed high gene flow levels. MostP. montanaclades were estimated to have diverged at 3.82–5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships inP. montana.