Species structure and phylogenetic relationships among the four currently recognised North Atlantic redfish species, Sebastes mentella (‘deep-sea’ and ‘oceanic’ phenotype), S. marinus (including ‘giant’ phenotype), S. fasciatus and S. viviparus, were investigated by sequencing the complete mitochondrial NADH dehydrogenase subunit 3 (ND3) gene for 313 individuals (333 including outliers). Low levels of sequence divergence of 0.3–2.3% between the North Atlantic Sebastes haplotypes, low resolution in phylogenetic trees and a star-like statistical parsimony network indicate a population bottleneck and/or founder event with a subsequent population expansion and a rapid speciation in North Atlantic Sebastes. Diagnostic mutations within the ND3 gene were recognised for some of the species. The results lead to the hypothesis that the ancestral haplotype lineage is now very rare or has suffered extinction and that the most basal lineage is found in S. viviparus. The results further indicate direct descendants in the S. fasciatus and S. marinus lineages from the S. mentella lineage, whereas the S. viviparus lineage originates from an earlier division. The observation of two haplotype lineages in S. marinus with a relatively high level of intraspecific genetic divergence, points towards a possible cryptic speciation.