Abstract: The whole chloroplast genome of Sphaerophysa salsula was sequenced and assembled based onIllumina high-throughput sequencing platform.The assembly result indicated that the whole chloroplast genomeof S.salsula had a total length of 123 327 bp,with a loss of IR region.The chloroplast genome encoded a total of108 genes,including 74 protein-coding genes,4 r RNA genes and 30 t RNA genes.and 99 SSR loci were found,and among them the number of mononucleotide,dinucleotide and trinucleotide repeat motifs was 75,17 and 7,respectively.The phylogenetic analysis results showed that S.salsula and Alhagi sparsifolia were sister species,which had the closest genetic relationship.The results would lay the foundation for the genetic diversity,population genetic structure and speciation mechanism of S.salsula in the future.