Styphnolobium japonicumis a significant resource of ornamental and medicinal plants. In this study, we employed high-throughput sequencing to assemble nine chloroplast genomes ofS. japonicum. We compared and reconstructed the phylogenetic relationships of these genomes, along with three publicly available chloroplast genomes. Our results showed that the length of the 12S. japonicumchloroplast genomes ranged from 158,613 bp to 158,837 bp, all containing 129 unique functional genes. The genetic diversity withinS. japonicumchloroplast genomes was relatively low, with π = 0.00029, Theta-W = 0.00028, and an indel frequency of 0.62 indels/1 kb. Among the four regions, the SSC region exhibited the highest genetic diversity and indel frequency, while the IR region had the lowest. Non-coding regions displayed greater genetic variation compared to coding regions, with a few highly variable regions identified. The phylogenetic tree constructed revealed that the major cultivars ofS. japonicumoriginated from two genetic ‘sources.S. japonicum‘JinhuaiJ2’ had an independent origin and showed close relatedness toS. japonicumvar.violacea,S. japonicumvar.japonicum, andS. japonicumf.oligophylla. On the other hand, other major cultivars shared a common genetic origin and were closely related toS. japonicumf.pendula. This study highlights the variability of chloroplast genomes withinS. japonicumand provides insights into the genetic origins of major cultivars and their relationships with different varieties and forma.