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Accurate species identification is required for stock assessment to monitor exploited species. Genetic tools are useful for species identification; employing SNP (single nucleotide polymorphisms) as markers, here we describe two cases of species misidentification which may lead to inaccurate estimates of stock size and adversely affect sustainable hake fisheries management in the Atlantic Ocean. North American hakes and African hakes show evidence of erroneous labelling that may obscure exploitation estimates of the species caught together in mixed fisheries (Merluccius albidus and Merluccius bilinearis, and Merluccius capensis and Merluccius paradoxus in North America and Africa respectively). Use of genetic methodology for species identification is recommended for improving accuracy of stock estimates in these two pairs of hakes.