•We sequenced the first complete chloroplast genome ofEugenia klotzschiana Berg.•The chloroplast genomes of the Myrteae tribe show a high level of conservation (sequence similarity and gene content), probably due to the recent diversification of the group.•For the first time, Eugenia klotzschianais included in a molecular phylogeny. Also, the combination of the two commonly used barcode loci, matK and rbcL, recovered some differences in the Myrtales tree topology when compared to the use of 61 plastid protein-coding genes combined.•Two plastid genes (rps12 and psaI) are under neutral evolution and the major number of mutational hotspots in chloroplast genomes from the Myrteae tribe occur in intergenic regions, except by the ycf1 gene. Myrteae is the most diversified tribe in the Myrtaceae family and has great ecological and economic importance. Here, we performed the assembly and annotation of the chloroplast genome of Eugenia klotzschiana O. Berg and used this in a comparative analysis with other 13 species from the Myrteae tribe. The E. klotzschiana plastome exhibited a length of 158,977 bp and a very conserved structure and gene composition when compared with other Myrteae genomes. We identified 34 large repetitive sequences and 94 SSR repeats in E. klotzschiana plastome. The trnT-trnL, rpl32-trnL, ndhF-rpl32, psbE-petL, and ycf1 regions were identified as mutational hotspots. A negative selection signal was detected in 74 protein-coding genes while neutral evolution was detected in two genes (rps12 and psaI). Furthermore, 222 RNA editing sites were identified in the E. klotzschiana plastome. We also obtained a plastome-based Myrtales phylogenetic tree, including E. klotzschiana for the first time in a molecular phylogeny, recovering its sister relationship for all other Eugenia species. Our results illuminate how evolution shaped the chloroplast genome structure and composition in the Myrteae tribe, especially in the E. klotzschiana plastome.