Whole genome duplication (WGD) is an important evolutionary mechanism that can facilitate adaptation and speciation. The Salmonidae (salmon, trout, and char) represent a useful model to study the effect of WGD due to the extensive diversity that has evolved following an autotetraploidization event in their common ancestor. Although most of the salmonid genome has become diploid post WGD, ~25% still display signals of tetrasomic inheritance. The genomic processes that lead to segmental polyploidy in otherwise diploidization of genomes are poorly understood. In salmonids, the systematic analysis of genome evolution among the major clades in the salmonid phylogeny is unclear due to the ~50 million-year divergence time between Salmoninae and the other salmonid lineages, largely because of the lack of genomic resources. To refine the understanding of the effects of the WGD in salmonids, female (20,450 loci) and male (6,340 loci) linkage maps were constructed for cisco Coregonus artedi. Homologous chromosomes were then identified among three coregonines and one representative species for each of Salmo, Salvelinus, and Oncorhynchus genera and the nonduplicated sister group of salmonids, Esox. Using this information, a cross-species comparison of homeologous regions was conducted to identify regions that still exhibit residual tetraploidy, that diploidized and diverged prior to speciation, and that diverged since diversification. The further development of genomic resources in less described salmonids will aid in understanding genomic variation among the salmonids post WGD. Furthermore, the linkage map will be used as a genetic resource that will facilitate research with the aim of determining the degree of heritable genetic differences among cisco forms.