The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus:Xylocarpus. Two of the three species of the genusXylocarpusare true mangroves (X. granatumandX. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of theseXylocarpusspecies along with two non-mangrove species of the Meliaceae family (Carapa guianensisandSwietenia macrophylla) and compared the genome features and variations across the five species.The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified inthe rpl22gene region only occurred inXylocarpus, while the repetitive sequences inaccDwere found inX. moluccensisandX. rumphii. TheTrnH-GUGandrpl32gene regions and four non-coding gene regions showed high variabilities betweenX. granatumand the two non-mangrove species (S. macrophyllaandC. guianensis). In addition, among theXylocarpusspecies, only two genes (accDandclpP) showed positive selection.Carapa guianensisandS. macrophyllaowned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove speciesX. rumphiiis closer toX. moluccensisthanX. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (threeXylocarpusspecies) and intergeneric (mangrove and non-mangrove genera) levels.