Abstract
Shads of the genus Alosa are essential to commercial fisheries across North America and Europe, but in some areas their species boundaries remain controversial. Traditional morphology‐based taxonomy of Alosa spp. has relied heavily on the number of gill rakers and body proportions, but these can be highly variable. We use mitochondrial (mt)DNA ( coI and cytb ) and genome‐wide single nucleotide polymorphisms (SNP) along with morphological characters to assess differentiation among endemic Ponto‐Caspian shads in the Sea of Azov. Morphological species assignments based on gill‐raker number were not congruent with genetic lineages shown by mtDNA and SNPs. Iterative analysis revealed that genetic lineages were associated with sampling location and several other morphometric traits (caudal peduncle depth, pre‐anal length and head length). Phylogenetic analysis of the genus placed Ponto‐Caspian Alosa spp. in the same evolutionary lineage as endangered Alosa spp. endemic to Greece, highlighting the importance of these findings to conservation management. We conclude that gill‐raker number is not reliable for delimiting species of Alosa. This taxonomic uncertainty should be addressed by examining type material to provide a robust integrative classification for these commercially important fishes.