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Macrocystis integrifolia, one species of brown alga, is one of the largest and most complex and dynamic ecosystems in the ocean, which can be also used as plant fertilizer. In the present study, the complete mitochondrial genome of M. integrifolia was reconstructed from whole genome Illumina sequencing survey data. The size of M. integrifolia mitochondrial DNA is 37,366 bp, including 3 rRNAs, 25 tRNAs, 35 proteins and 2 ORFs. The phylogenetic tree, which was established based on mitochondrial genomes of brown algae, indicated that M. integrifolia is at an earlier stage of differentiation in Laminariaceae.