Thoracotremata is a group of Brachyura, with 1,248 extant species. To date, parts of the thoracotreme phylogeny are not yet resolved and require further investigation. In this study, 12 new mitogenomes from the four thoracotreme superfamilies were sequenced. They contain a standard set of 37 genes, and vary in size from 15,422 (Hapalocarcinus marsupialis Stimpson, 1858 sensu lato) to 16,490 bp [Arcotheres sinensis (Shen, 1932)]. Combined with 58 thoracotreme mitochondrial genomes (mitogenomes) from GenBank, we described the evolution of gene rearrangement and the internal phylogenetic relationships of Thoracotremata, and evaluated the phylogenetic position of Cryptochiroidea and Pinnotheroidea. Nine distinct patterns of mitochondrial gene order (MGO) among thoracotreme mitogenomes are identified, with four MGOs newly found in Thoracotremata. All other gene orders are the result of transformational pathways originating from brachyuran gene order (BraGO). The different gene orders have variable levels of gene rearrangements, which involve both tRNAs and protein-coding genes. No link between variable gene arrangements (breakpoint distances) and nucleotide substitution rates (branch lengths) is found in thoracotreme crabs. The symbiotic groups, the cryptochiroid and pinnotheroid crabs, display variable MGOs (CryGO, Pin1GO, and Pin2GO), providing evidence for possible correlations of rearranged MGOs to the adaptations to specialized lifestyles. In our phylogenetic analyses, Cryptochiridae (Cryptochiroidea) show close relationship with an Ocypodoidea lineage (Camptandriidae/Xenophthalmidae/Dotillidae). Pinnotheridae (Pinnotheroidea) form the basal monophyletic clade.

Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda & Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species.