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Brasenia schreberi is a perennial aquatic herb. We determined the complete chloroplast genome sequence for B. schreberi using Illumina sequencing data. The complete chloroplast sequence is 158,993 bp, include large single-copy (LSC) region of 88,779 bp, small single-copy (SSC) region of 21,665 bp, a pair of invert repeats (IR) regions of 21,078 bp. Plastid genome contains 132 genes, 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis base on 12 chloroplast genomes indicates that B. schreberi is sister to Cabomba spp. in Cabombaceae.