Astragalusis the largest flowering plant genus. We assembled the plastid genomes of fourAstragalusspecies (Astragalus iranicus,A.macropelmatus,A.mesoleios,A.odoratus) using next-generation sequencing and analyzed their plastomes including genome organization, codon usage, nucleotide diversity, prediction of RNA editing and etc. The total length of the newly sequencedAstragalusplastomes ranged from 121,050 bp to 123,622 bp, with 110 genes comprising 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Comparative analysis of the chloroplast genomes ofAstragalusrevealed several hypervariable regions comprising three non-coding sites (trnQ(UUG)–accD,rps7 –trnV(GAC) andtrnR(ACG)–trnN(GUU)) and four protein-coding genes (ycf1,ycf2,accD andclpP), which have potential as molecular markers. Positive selection signatures were found in five genes inAstragalusspecies includingrps11,rps15,accD,clpP andycf1. The newly sequenced species,A.macropelmatus, has an approximately 13-kb inversion in IR region. Phylogenetic analysis based on 75 protein-coding gene sequences confirmed thatAstragalusform a monophyletic clade within the tribe Galegeae andOxytropisis sister group to the Coluteoid clade. The results of this study may helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genusAstragalusand IRLC levels and investigating the phylogenetic relationships. Moreover, the newly plastid genomes sequenced have been increased the plastome data resources onAstragalusthat can be useful in further phylogenomic studies.