The complete plastome size of Citrus hystrix DC. 1813 was 159,893 bp in length and has a typical quadripartite structure. The 87,148-bp-long large single-copy and the 18,763-bp-long small single-copy regions were separated by a pair of inverted repeats (each 26,991 bp). The plastome was predicted to contain 132 genes, of which 87 were CDS, 37 were tRNA, and eight were rRNA genes. The plastome was A/T biassed, and the overall GC content was 38.4%. Using maximum likelihood and Bayesian inference methods, the phylogenetic analysis of the complete plastome sequence revealed a close relationship between C. hystrix and C. aurantiifolia, placing them under the same clade as C. micrantha.