In this study, the chloroplast complete genomes of Ammopiptanthus mongolicus and Ammopiptanthus nanus were used as research objects, and their genomic structure and phylogenetic relationship were compared and analyzed. The results showed that: (1) the chloroplast genomes of A. mongolicus and A. nanus have a typical foursegment structure, with total length of 153 935 and 154 140 bp. Among them, the large singlecopy region (LSC) is 83 891 and 84 126 bp, and the small singlecopy region is 18 022 and 18 014 bp (SSC), respectively. The pair of inverted repeat regions (IRs) with lengths of 26 011 and 26 000 bp, respectively. The chloroplast genomes of A. mongolicus and A. nanus have annotated 130 genes, including 85 proteincoding genes, 37 tRNA genes and 8 rRNA genes. (2) 26 and 15 palindromic repeats, 39 and 50 tandem repeat, 23 and 34 dispersed palindromic repeats were detected in the chloroplast genomes in the two species. At the same time, 96 SSRs were identified in the chloroplast genomes of A. mongolicus and A. nanus, of which 74 and 73 were mononucleotides, 5 and 6 were dinucleotides, and 17 were compound SSR. Boundary analysis shows that the IR region between A. mongolicus and A. nanus is similar, but there are still some differences. (3) A phylogenetic tree was constructed from the chloroplast genomes of 17 species of Papilionoideae, and 2 species of Caesalpinioideae, using the neighborjoining method (NJ). The phylogenetic tree showed that A. mongolicus and A. nanus were clustered into independent branches with higher support. This study provides a theoretical basis for further studies on interspecific identification, development of SSR molecular markers, conservation work, population dynamics, and further study of the evolution process of the Trib. Podalyrieae.