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Ipomoea aquatica, commonly known as water spinach, is an edible annual vegetable in the genus Ipomoea,. In this study, the complete plastome of Ipomoea aquatica was determined using the Illumina sequencing platform. The plastome size was 162,663 bp. It consists of four regions, including a large single-copy region (88,166 bp), a small single-copy region (12,069 bp), and a pair of inverted repeat regions (31,214 bp). This plastome encodes 114 unique genes, including 80 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and 4 ribosomal RNA genes (rRNAs). The GC content was 39.1%. Phylogenomic analysis based on 19 complete plastomes revealed that I. aquatica was closely related to I. diamantinensis.