Greenland halibut (Reinhardtius hippoglossoides) is a commercially important species in the North Atlantic whose spatial population structure has not yet been fully determined. To help resolve this issue further, we genotyped individuals from across the North Atlantic using a subset of previously identified, informative single nucleotide polymorphic (SNP) markers. We assessed the population genetic structure in the species in the largest part of its range using these SNPs, but also considered the impacts of sex association in the markers. We observed an important influence of sex in a proportion of the loci which would likely confound signals of population structure made using them. The use of a SNP set with sex-associated loci removed showed a longitudinal pattern with two major clusters but with high levels of admixture. The results support weak genetic structuring in this species following an isolation by distance pattern. The study discusses the consequences of ignoring sex when assessing population structure, particularly in species with high sexual dimorphism.