Durian, or Durio zibethinus, is an exotic fruit with high economic value in Southeast Asia. This study aims to determine the genetic variants based on the chloroplast genome between species and cultivars in the Durio genus and design the molecular marker based on microsatellite resources. The research was conducted by collecting the data of 8 chloroplast genomes followed by the genome structure and organization analysis, variants analysis, phylogenetic relationship analysis, and possibly, primer designing. Overall, the results showed that regions with high Pi values for the nucleotide diversity analysis were the regions in ycf1, psbZ-rps14, accD, and rpl33-rps18. Although the nucleotide diversity analysis had shown various hotspots from the current data of complete chloroplast genomes of the Durio genus, the accD region showed to have a high Pi value between species but failed to distinguish between variants of the same species. Furthermore, 13 primer SSR regions were selected from 135 SSRs, and the corresponding primer pairs were designed for amplification. Durio zibethinus cv. Ri6 has a close relationship to other Durio zibethinus cultivars but has high genetic divergence from other Durio genus species. The Durio genus had a close relationship to Reevesia genus according to the phylogenetic tree of Malvaceae family. The cp genomes are stated to be a useful tool in studying the phylogenetic relationship. In conclusion, the cp genomes are a useful tool and could be further utilized for molecular markers designing, the evolution history of the Durio genus.