Taxonomy and phylogenetic relationships of Paguroidea (Anomura) have long been a subject of controversial. The complete sequence of mitochondrial genomes (mitogenomes) can provide valuable information for resolving these contentious issues related to species identification and phylogeny. In this study, the complete mitogenome sequence of Dardanus hessii
(Paguroidea: Diogenidae) was sequenced and analyzed for the first time. Additionally, it was compared with 16 other published Paguroidea mitogenomes. All the Paguridea mitogenomes contain 37 genes and one long non-coding control region. Analysis of mitochondrial genome similarity and collinearity analysis showed that all 17 Paguroidea mitogenomes had undergone gene rearrangement events. These rearrangements can be divided into seven types, including four types in Paguridae, two types in Diogenidae and one type in Pylochelidae. Genetic distance, sequence similarity and phylogenetic tree demonstrated that Pagurus japonicus
and Pagurus filholi
were the same species, implying that at least one of the species was misidentified. The phylogenetic tree also showed that not all Diogenidae species clustered within a single clade, as Clibanarius infraspinat
us clustered together with Coenobitidae species, indicating that Diogenidae may be a paraphyletic group. These results contribute to a better understanding of mitochondrial gene rearrangement and phylogeny of Paguroidea, and provide insights into the applicability of mitochondrial gene rearrangement as a molecular marker for phylogenetic study.