BackgroundElaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking.MethodsTo understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated withElaeocarpus japonicusandSloanea sinensis(family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software.ResultsThe results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes ofElaeocarpus,Sloanea,CrinodendronandVallealacked therpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked thendhK gene inElaeocarpus,Vallea stipularis, andAristotelia fruticosa. The LSC region of the chloroplast genomes lacked theinfA gene in genusElaeocarpusandCrinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species.Rps3 was detected in the neighboring regions of the LSC and IRb regions inElaeocarpus. (d) Phylogenomic analysis revealed that the genusElaeocarpusis closely related toCrinodendron pataguaon an independent branch andAristotelia fruticosais closely related toVallea stipularis, forming a clade with the genusSloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genusElaeocarpusdiverged 53 Mya and that the genusSloaneadiverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.