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The complete mitochondrial genome of mangrove plant: Bruguiera sexangula (Lour.) Poir. var. rhynchopetala Ko was analyzed in this paper, which is the first for the genus within the family Rhizophoraceae. The mitogenome sequence is 286,503 bp in length containing three ribosomal RNA genes, 25 transfer RNA genes, and 35 protein-coding genes. Genes ccmFc, rps3 and cox2 contain one intron, gene nad5 contains two introns, genes nad1 and nad4 contain three introns, and genes nad2 and nad7 contain four introns. Genes nad1, nad2 and nad5 are trans-splicing genes. Phylogenetic analysis using the maximum-likelihood method positioned Bruguiera × rhynchopetala closely with Citrus sinensis in Rosales.