The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.

完整的线粒体基因组为理解基因重排、分子进化和系统发育分析提供了重要信息。在这里，我们首次确定了Gonatopsis borealis和Onychoteuthis Compacta的完整线粒体基因组序列。它们的基因组大小分别为20,148 bp和20,491 bp，包括18个蛋白质编码基因、COI-COIII、ATP6和ATP8重复，23个转移RNA基因和2个核糖体RNA（rRNA）基因（12S和16S rRNA）。具体来说，总体A+T含量为70.69%和72.67%。它显示出显着的 AT 偏差。整个有丝分裂基因组显示正 AT 偏度（0.070 和 0.062）。此外，Oegopsida 内的基因顺序已重新排列。串联重复随机丢失模型被确定为最有可能解释观察到的基因重排。进行系统发育分析，发现结果树与形态学鉴定分类一致。对35个物种的分化时间的估计表明，Oegpsida的主要分化发生在140.70 Mya。这些结果将有助于更好地了解G.borealis和O.compacta的基因重排和进化，并为进一步的Oegopsida系统发育遗传学研究奠定基础。