Abstract
A novel method of single nucleotide polymorphism (SNP) analysis in fishes [glycosylase mediated polymorphism detection (GMPD)] was applied, for the first time in any fish species, to polymorphisms present in the Atlantic cod Gadus morhua mtDNA D‐loop and nuclear transferrin genes. The utility of the GMPD technique for population genetics of Atlantic cod is highlighted, since significant haplotype frequency differences were observed between Baltic and Atlantic samples of cod at a D‐loop SNP and allele frequencies differences between west and east Atlantic samples at an SNP located in the transferrin gene.