Syzygium samarangense is an important fruit of Myrtaceae family and commercially planted in tropical areas of the world. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of S. samarangense for the first time (accession number of MH371141). The chloroplast genome is 159,109 bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,533, 18,882, and 25,847 bp long, respectively. Phylogenetic tree analysis exhibited that S. samarangense was clustered with other Myrtaceae species with 100% bootstrap values.