Boreogadus saida (Polar cod) is a critical ecological linkage between planktonic primary production and megafaunal top consumers in the Arctic. Despite its critical ecology, the population structure, especially the relationship between fjord and oceanic groups inhabiting environments with different physical characteristics, is poorly described. Though the subject of several genetic studies, an underlying biological basis for this difference is yet to be identified. Total RNA was extracted from liver tissue of 144 Polar cod representing 3 pairs of neighboring fjord and offshore populations, comprising a North-South gradient of Eastern Greenland and Svalbard. 3’ sequencing of the corresponding cDNA on two Illumina HiSeq 4000 lanes yielded approximately 14 million reads per sample upon which differential gene expression analysis was performed. After alignment and read quantification using the Atlantic Cod (Gadus morhua) genome, approximately 2,000 significantly differentially expressed (up or down regulated) genes per fjord-offshore pairing were identified. Gene ontology profiling of the differentially expressed genes by biological process revealed that distance between fjord and offshore populations is a strong predictor of gene expression between these populations. The differentially expressed biological pathways identified provide insight on the origin and structure of fjord and oceanic populations of Polar cod including evidence of gradual differentiation within the Greenland Sea based primarily on distance from the coast. This examination of a key Arctic species through the lens of a novel transcriptomic approach provides new context to previous genetic investigations as well as a unique foundational dataset for subsequent analyses of these populations
