Phylogenetics is the important study of evolutionary relationships of all organisms. This study was conducted to investigated and reconstructed the phylogenetic relationships amongst 15 durian (Durio spp.) species using bioinformatics analysis of 5.8 S rRNA genes and Internal Transcribed Spacer (ITS1 & ITS2) regions. In Silico methods was used for analysis the phylogenetic relationships of those germplasm with several online sofwares, such as BLAST, Align, ClustalW, and TreeView. The results showed that 15 Durio species were grouped into three main distinct clusters or groups. Based on this result, D. griffithii and D. grandiflorus were the durians of most closely related, with 99% of similarity index. Meanwhile, Durio zibethinus has closely related to D. lowianus, with 98, 9% of similarity index. These information might be useful for conservation and management strategies of durian germplasm, especially on the progress of durian breeding program.