This population genomics project focuses on low-coverage whole-genome sequencing of individuals representing distinct morphs of Arctic charr from two Icelandic and two Norwegian lakes. These morphs inhabit the limnetic and benthic zones of the lakes, and their phenotypes and ecological behaviors have been extensively characterized in previous studies. Moreover, the pioneering genetic studies based on a small proportion of markers provided a general overview of the genetic structure of the charr morphs. The aim of this research is to re-investigate the genetic basis of sympatric differentiation in Arctic charr by leveraging whole-genome data, offering a more detailed and updated genomic perspective on morph differentiation. The four lakes included in this study display varying degrees of genetic differentiation among charr morphs. These range from a lake with minimal or no genetic divergence to one exhibiting strong genetic differentiation with ongoing gene flow and another where pronounced genomic differentiation suggests complete or near-complete reproductive isolation.