<p>This study investigates the evolutionary dynamics of the plastome by presenting a comprehensive analysis of the de novo sequenced Thevetia peruviana plastome, along with a comparative evaluation of 85 plastomes from species within the Apocynaceae family. We examined genome structure, gene length variability, nucleotide diversity, and evolutionary dynamics to better understand this plant family’s genetic architecture and adaptive evolution. The study confirmed the typical quadripartite structure of the <i>T. peruviana</i> plastome, with significant variations observed in the small single-copy (SSC) region, suggesting its adaptive role. Gene length analysis revealed lineage-specific variations, notably in <i>psb</i>L, <i>ycf</i>1, and <i>acc</i>D, linked to functional shifts in photosynthesis and protein synthesis. Analysis of nucleotide diversity and Ka/Ks ratios revealed a complex interplay between purifying selection (<i>ndh</i>B involved in maintaining chloroplast stability) and positive selection (<i>ycf</i>2 involved in adaptive evolution) across the genomes. Phylogenetic analysis confirmed a close relationship between <i>Thevetia</i> and <i>Allamanda</i> while highlighting distinct clades corresponding to ecological niches, such as epiphytes and drought-adapted shrubs. This study provided insights into the role of plastome variations in adaptation and evolution within Apocynaceae, contributing to a deeper understanding of their ecological diversification and evolutionary history. Our work contributes to the broader understanding of plastome evolution in angiosperms, with implications for future plant adaptation, functional genomics, and evolutionary biology studies.</p>