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Citrus aurantium (C. aurantium), belonging to the family Rutaceae, is usually utilized as a flavoring and acidifying agent for food. This study assembled and characterized the complete chloroplast (cp) genome of C. aurantium. The cp genome was 160,140 bp in length, containing a pair of inverted repeats (IRs, 26,996 bp each), which is separated by a large single-copy (LSC, 87,763 bp) region and a small single copy (SSC, 18,385 bp) region. The cp genome has overall GC content of 38.48% and 135 genes, composing of 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 25 cp genomes highly supported that C. aurantium was evolutionarily close to Cirtus sinensis (C. sinensis).