The Knysna seahorse Hippocampus capensis Boulenger, 1900 was the first seahorse species listed as endangered on the IUCN Red List due to its limited distribution range, small population size and vulnerability to natural and anthropogenic disturbances. In the present study, the complete mitogenome of H. capensis was determined. It is 16,529 bp in length and contains 13 protein-coding (PCG) genes, 22 tRNA genes, two rRNA genes, one origin of replication on the light-strand (OL) and a control region (CR). The overall base composition is 32.46, 29.48, 23.35 and 14.71% for A, T, C and G, respectively, with a slight AT bias of 61.93%. The 13 PCGs encode 3798 amino acids in total, most of which use the initiation codon ATG except COX1 starts with GTG. Seven genes applied TAA or TAG as the stop codon, except ND2, COX2, COX3, ND3, ND4 and Cytb use an incomplete stop codon T. The lengths of 12S rRNA and 16S rRNA are 937 and 1696 bp, respectively. Phylogenetic tree analysis based on the complete mitochondrial genome suggests H. capensis is closely related to the kuda complex species H. kuda and H. reidi. This work provides fundamental molecular data which will be useful for species identification, forensic genetics and further management and conservation of this endangered marine fish.