The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.

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