Abstract: The generic delimitation of the Caesalpinia group continues to be under contention, similar to several other lineages of the hyper diverse legume family. Despite its ecological and economic importance and role as a model to explore correlations between ecological diversification and genomic traits, intergeneric and infrageneric relationships remain unresolved, even after recent phylogenetic analyses. While phylogenomic approaches have elucidated complex relationships within the angiosperm tree of life, the phylogenetic backbone of the Caesalpinia group remains poorly defined owing to limited genomic data. To address this gap, we combined de novo assembled plastomes from 19 samples across nine genera, along with 27 previously published plastomes, resulting in 46 plastomes from 16 of the 26 genera. The phylogenomic analysis generated a robust phylogenetic hypothesis, distinguishing two main clades, one in the Neotropics and the other Pantropical, and resolving several previously ambiguous relationships. Notable changes in plastome gene content were observed, including six gene losses (psbL, rpl22, rps2, rpl32, ycf1, ycf2) and duplications (ndhB, rpl23, rps7, rps12, ycf1, ycf2). Other changes included shifts in inverted repeat (IR) boundaries and genome rearrangements, indicating lineage-specific plastome evolution. Hypervariable regions were identified as potential mini-barcodes, with cpSSRs providing valuable resources for species delimitation and population genetics studies. Codon usage revealed a strong AT bias and relaxed purifying selection in genes like accD, clpP, and rps16. These findings offer novel insights into Caesalpinia group evolution, emphasizing plastome data’s utility for resolving complex evolutionary questions and establishing a genomic toolkit for future research on the systematics, conservation, and evolutionary biology of legumes

Key words: Phylogenomics, Generic flux, Gene duplications, Gene loss, Genomic variation, Ecological adaptation, Species delimitation, Conservation genomics