Syzygium grijsii, an evergreen shrub of Myrtaceae and Syzygium, has good prospects for exploitation, but its chloroplast genome characteristics and phylogenetic relationships have not been reported. To fill the gap in the genomics of S. grijsii, a systematic study of the chloroplast genome of S. grijsii was conducted in this paper. Illumina high-throughput sequencing was used to perform complete assembly in the GetOrganelle platform, and the assembled data were also used to analyze the structural features and phylogenetic relationships of the S. grijsii chloroplast genome, including the structure, function and characteristics of the S. grijsii chloroplast genome, codon preference analysis, comparative analysis of the chloroplast genome and phylogenetic analyses. The results were as follows:(1)The chloroplast genome of S. grijsii was 158 591 bp in size, which contained 129 genes. Among them, 8 were rRNA genes, 37 were tRNA genes and 84 were protein-coding genes. The analysis detected 39 repetitive sequences and 84 SSR loci.(2)Codon preference analysis revealed that there was a bias towards A/U at the ends of the S. grijsii chloroplast genome, and the most used codon was the one encoding leucine.(3)In comparison with closely related species, the boundary length of S. grijsii was conserved, and the gene species at the boundary were similar to several Syzygium species; the S. grijsii chloroplast genome had a high degree of variability in the LSC and SSC regions, with 45 sites of 0.010 < Pi < 0.015 and a high level of nucleotide diversity.(4)Phylogenetic analysis showed that S. grijsii was most closely related to S. jambos, S. forrestii and S. cumini, followed by S. malaccense. The study concluded that S. grijsii had a conserved chloroplast genome structure with distinct features, sequence similarity and nucleotide diversity compared to Syzygium species, and affinity between it and various Myrtaceae species. In this paper, the genomic characterization and phylogenetic analysis of the chloroplast genome of S. grijsii are conducted to lay the theoretical foundation for the identification and exploitation of the germplasm resources of S. grijsii. [ABSTRACT FROM AUTHOR]