| Summary: | The genus <i>Gueldenstaedtia</i> belongs to Papilionaceae’s inverted repeat-lacking clade (IRLC) and includes four species distributed throughout Asia. We sequenced the chloroplast genome of <i>G. verna</i> and compared it with those of the IRLC clade. The genome was 122,569 bp long, containing 77 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analyses showed that <i>G. verna</i> lost one inverted repeat region, the <i>rps16</i> gene, an intron of <i>rpoC1</i>, and two introns of <i>clpP</i>. Additionally, <i>G. verna</i> had four inversions (~50 kb inversion, <i>trnK</i>–<i>psbK</i>; ~28 kb inversion, <i>accD</i>–<i>rpl23;</i> ~10 kb inversion, <i>rps15</i>–<i>trnL</i>; ~6 kb inversion, <i>trnL–trnI</i>) and one reposition (<i>ycf1</i>). Its G + C content was higher than that of other IRLC species. The total length and number of repeats of <i>G. verna</i> were not significantly different from those of the other IRLC species. Phylogenetic analyses showed that <i>G. verna</i> was closely related to <i>Tibetia</i>. A comparison of substitution rates showed that <i>ycf2</i> and <i>rps7</i> were higher than one, suggesting that these were positive selection genes, while others were related to purified selection. This study reports the structure of the chloroplast genome of a different type, i.e., with four inversions and one reposition, and would be helpful for future research on the evolution of the genome structure of the IRLC.
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