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The Indo-Pacific nassariids (genus <i>Nassarius</i>) possesses the highest diversity within the family Nassariidae. However, the previous shell or radula-based classification of <i>Nassarius</i> is quite confusing due to the homoplasy of certain morphological characteristics. The toxin accumulators <i>Nassarius glans</i> and <i>Nassarius siquijorensis</i> are widely distributed in the subtidal regions of the Indo-Pacific Ocean. In spite of their biological significance, the phylogenetic positions of <i>N</i>. <i>glans</i> and <i>N</i>. <i>siquijorensis</i> are still undetermined. In the present study, the complete mitochondrial genomes of <i>N</i>. <i>glans</i> and <i>N</i>. <i>siquijorensis</i> were sequenced. The present mitochondrial genomes were 15,296 and 15,337 bp in length, respectively, showing negative AT skews and positive GC skews as well as a bias of AT rich on the heavy strand. They contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, and their gene order was identical to most caenogastropods. Based on the nucleotide sequences combining 13 protein coding genes and two rRNA genes, a well-supported phylogeny of <i>Nassarius</i> was reconstructed, and several morphological synapomorphies were observed corresponding to the phylogenetic framework. In addition, the sister group relationship between <i>N. variciferus</i> and the remaining toxin-accumulated nassariids was determined, suggesting that the phylogeny might be related to their diet. The divergence time estimation analysis revealed a correlation between speciation events of nassariids and glacial cycles during the Pliocene-Pleistocene epoch.