A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden setup to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control. KEYWORDS Life-history strategies RADseq GWAS salmonids Genome-wide association studies (GWAS) aim to reveal links between genotypes and phenotypes. Originally developed for case-control comparisons in medical sciences (Ku et al. 2010), association mapping has been subsequently adopted for use on other organisms and for addressing agricultural, evolutionary and ecological questions. Recent studies have described genetic determinants for economically and ecologically important traits. For example, vgll3 locus affects maturation age in Atlantic salmon Salmo salar in sex-dependent fashion (Ayllon et al. 2015; Barson et al. 2015) and greb1l affects migration timing in Pacific salmonids Onchorynchus spp. (Prince et al. 2017). These studies have revealed that traits that were traditionally thought to be influenced by tens or hundreds of genes (Waples et al. 2004; Johnston et al. 2014; Gutierrez et al. 2015) can actually be influenced by loci with major effect. Identification of these genotype-phenotype associations have helped to further understand the evolution of these traits in response to both natural and human-induced selection pressures (Czorlich et al. 2018). Salmonids display a variety of anadromous and potamodromous migratory strategies with populations ranging from fully resident to fully