Complete mitochondrial genomes of Pinctada fucata martensii and Pteria penguin were sequenced. The P. fucata martensii mitogenome was 31,435 bp long, which made it the longest genome so far published in the Pinctada and Pteria. The mitochondrial genome of P. penguin lacked three transfer RNA (tRNA) genes and had one duplicated tRNA gene; this mitogenome has the fewest tRNA of any mitogenome so far available in the Pinctada and Pteria. Both mitogenomes were strongly skewed away from C in favor of G and away from A in favor of T. The mitogenomic gene order in these two species was incongruent with mitogenomic gene orders for other species of Pteriomorphia, and Pteria penguin was placed as sister to all other Pinctada species. This study provided insights into the evolutionary relationships among Pteriidae species.