Ischnochiton hakodaensis is one of Polyplacophora species, which plays an important role in the intertidal and subtidal ecosystems. In this study, the complete mitochondrial genome of I. hakodaensis was obtained with 15,139 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes. The overall base composition of the genome is 35.93% A, 13.51% G, 37.19% T, 13.38% C. The phylogenetic tree show that I. hakodaensis, Acanthopleura brevispinosa, Acanthopleura granulate, and Liolophura japonica constituted a sister clade along with Tonicia forbesii and Tonicia lamellose.