In this study, the authors sequenced and characterized the complete mitochondrial (mt) genomes of two hard ticks of the genus Ixodes, I. nipponensis and Ixodes (Pholeoixodes) sp., which were 14 505 and 14 543 bp in length, respectively. Their mt genomes encoded 37 genes, including 13 protein‐coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, and have only one non‐coding region. The gene order in their mt genomes was the same as that of other Ixodes spp. mt genomes. The average sequence identity, combined nucleotide diversity, non‐synonymous/synonymous substitutions ratio analyses consistently demonstrated that cox1, rrnS, cox2, cox3 and cytb were the most conserved and atp8, nad6 and nad2 were the most variable genes across Ixodes mitogenomes. Phylogeny of the present Ixodes spp., and other selected hard tick species, based on concatenated amino acid sequences of PCGs, confirmed their position within the genus Ixodes and sub‐family Ixodinae. The novel mt markers described herein will be useful for further studies of the population genetics, molecular epidemiology and systematics of hard ticks. This study sequenced and characterized the complete mitochondrial (mt) genomes of two hard ticks of the genus Ixodes, I. nipponensis and Ixodes (Pholeoixodes) sp.. Two Ixodes ticks mt genomes encoded 37 genes. This study provided molecular data for Ixodes (Pholeoixodes) sp., which is a taxonomically controversial species.