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Pleurosigma inscriptura M. A. Harper is a marine diatom in Naviculales (Bacillariophyceae) order distributed in New Zealand, South America, Argentina, and Korea. We assembled the complete mitochondrial genome sequence of Pleurosigma inscriptura (38,013 bp), and annotated 34 protein-coding genes, 25 transfer RNAs, and 2 ribosomal RNAs. We analyzed a maximum-likelihood tree using conserved 34 mitochondrial genes from Bacillariophyta species. In the mitochondrial phylogeny, P. inscriptura showed a strong monophyletic relationship with Haslea nusantara and Navicula ramosissima.