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The complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus  Exhippolysmata  (i.e.,  Exhippolysmata ensirostris ) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the  E. ensirostris  mitogenome had a typical cloverleaf secondary structure, except for  trnS1  (AGN), which appeared to lack the dihydrouridine arm. The gene order in the  E. ensirostris  mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of  trnL2 - cox2  changed to  cox2 - trnL2 . The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of  E. ensirostris . The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of  E. ensirostris  and lay a foundation for further phylogenetic studies of Caridea.

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The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea