This study examines genome evolution in the Salmonidae, focusing on the implications of whole-genome duplications (WGDs) and subsequent gene fractionation. By leveraging sequence similarity to infer key evolutionary parameters, such as gene fractionation rates, the research addresses the complexities using the ‘syntenic crumble’ phenomenon, which complicates the analysis of older polyploidization events due to the gradual disintegration of synteny blocks over time. A series of statistical analyses, along with a branching process model to assess duplicated gene pairs, are employed to refine the methodology, incorporating the analysis of unpaired genes—a technique adapted from plant genomics. Results demonstrate distinct gene retention and loss patterns following polyploidization, with notable differences in the ‘crumble constant’ (c). Analysis of synteny blocks across various salmon datasets underlines the impact of block size criteria on genomic evolution, pointing to species-specific evolutionary trajectories.