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The genus  Palaemon  comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species.  Palaemon  is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several  Palaemon  species, being the clearest evidence in the European rockpool shrimp  P .  elegans . Here we sequenced and described seven European  Palaemon  mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other  Palaemon  species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within  P .  elegans . The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus  Palaemon  and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in  Palaemon  and crypticism in  P .  elegans  was confirmed. Mitochondrial genome and  cox1  (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between  P .  elegans  and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of  P .  elegans . On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp  P .  serratus  was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus  Palaemon  seems to be a common phenomenon.

Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans