Abstract [Objective] To compare the genetic diversity and relationships between the chloroplast genomes of olive varieties selected and bred in China and those in the Mediterranean olives, and to estimate the maternal diversity of olive varieties selected and bred in China, and in turn provide a basis for the development of Chinese olive accession. [Methods] NOVOPlasty v.4.3.1 was used to assemble chloroplast genomes, which were based on the genome re-sequencing data of the nine olive varieties selected and bred in China and seven Iranian accessions, both of which were sequenced in this study, and fifty-two Mediterranean olive accessions downloaded from the database, and then calculated the sequence polymorphism; GPA, RAxML-NG, and Network 5.0 and other software were used to construct the chloroplast genome map, the relationships of phylogeny and network of haplotype respectively. [Results] The chloroplast genomes of the analyzed olive accessions were consistent in terms of tetrad structure and number of genes in this study. All chloroplast genomes identified seventeen haplotypes, among which, the olive varieties selected and bred in China have only one haplotype which share with the most cultivated olives. The oleasters have the highest genetic diversity, followed by the cultivated olives and then Iranian accessions, while nine olive varieties selected and bred held all genetic diversity of 0. The phylogenetic relationship was consistent with the network of haplotype, one branch includes the most of the cultivated varieties, Iranian olive accessions and all olive varieties selected and bred in China. [Conclusion] The nine olive varieties selected and bred in China showed an extremely low diversity of maternal origin. It is necessary to select and breed the olive varieties adapted to China’s habitats from a more comprehensive lineage of olive accession in the later stages.