The complete mitochondrial genome (mitogenome) of a red alga, Pyropia haitanensis Chang et Zheng, a circular-mapping molecule, was determined to be 37,023 bp. The overall AT content of the mitogenome is 69.32%. It contains 54 genes, including 49 conserved genes, 4 intronic reading frames, and an additional free-standing open reading frame. The rnl gene and cox1 gene are the only two interrupted genes in the mitogenome. All the protein-coding genes and Open Reading Frames (ORF) have typical ATG start codon, except for cox1 and cox2, which contain the unusual GTG and CTG as an initiator codon, respectively. Relative differences are found by comparing the mitogenome of P. haitanensis with that of Porphyra purpurea, reinforcing the viewpoint that the two species belong to different genus.