Genome duplication can provide material for evolutionary innovation, and much remains unknown about its functional effects. Assembly of large, outbred eukaryotic genomes is difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species. However, these methods often result in a low number of homologous markers between species due to phylogenetic distance or technical differences in library preparation. Family Salmonidae is ideal for studying the effects of whole genome duplication. The ancestral salmonid underwent whole genome duplication around 65 million years ago and the tetraploid genome has undergone rediploidization during the salmonid diversification. In the salmonids, synteny occurs between orthologous chromosomes, but each species exhibits conserved and unique chromosome arm fusions and fissions. In this study, we identify orthologous chromosome arms within the salmonids using available RADseq salmonid linkage maps along with a new high-density linkage map (3826 markers) constructed for the Salvelinus genera (Brook Charr S. fontinalis). We developed MapComp, a program that identifies identical and proximal markers between linkage maps using a reference genome of a related species as an intermediate (e.g. Rainbow Trout Oncorhynchus mykiss). We greatly increased the number of comparable markers between linkage maps relative to that obtained using only identical markers. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-whole genome duplication in five species of Oncorhynchus, and one species of each of Salvelinus, Salmo, and Coregonus, representing all of the main salmonid genera. Additionally, integration with the genetic map of the pre-duplicated sister species Northern Pike Esox lucius permitted the identification of homeologous chromosomes in all species. Putative conserved inversions within chromosome arms were also identified among species. Analyses of RADseq-based linkage maps from other taxa are likely to benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/.