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The brown mussel Perna pernais widely distributed along the east coast of Algeria, and it is receiving much attention from researchers working in the field of pollution monitoring. However, this species is frequently confused with other Mytilidae species, in particular, with the Mediterranean mussel Mytilus galloprovincialis. This study is the first to identify mussels collected from four different sites in Northeastern Algeria, using both morphological characters and molecular analysis of the mitochondrial 16S rDNA gene sequences. The obtained results revealed that morphological and molecular identification coincided, and all samples belonged to P. pernaspecies. Further phylogenetic analysis showed Perna species group in a single branch which is more closely related to the branch of Mytilusspecies than the other representative Mytilidaespecies. These research findings will be helpful for the accurate identification of the brown mussels and their sustainable use and management.