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<i>Cyperus esculentus</i> produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated <i>C. esculentus</i> (var. <i>sativus</i> Boeckeler). The results showed that the complete chloroplast genome of <i>C. esculentus</i> was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of <i>C. esculentus</i>. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four <i>Cyperus</i> species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five <i>Cyperus</i> species within the Cyperaceae formed a clade, and <i>C. esculentus</i> was evolutionarily more related to <i>C. rotundus</i> than to the other three <i>Cyperus</i> species. In summary, the chloroplast genome sequence of the cultivated <i>C. esculentus</i> provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other <i>Cyperus</i> species in the Cyperaceae family.