The related species, marble (Salmo marmoratus) and brown trout (Salmo trutta), have a different skin pigment pattern. While marble trout is characterized by labyrinthine skin pattern, spotted skin pattern with black and red spots is typical for brown trout. Through extensive bioinformatic analysis and the availability of a well-annotated brown trout genome, we have gathered a large number of genes with non-synonymous mutations that may be candidate genes for pigmentation. Among all identified polymorphisms between marble and brown trout, candidate single-nucleotide polymorphisms were selected for laboratory validation and further research. By analysis using the KEGG biological pathway collection, the candidate genes were distributed among the biological pathways. The pathways with the highest number of such genes were: (1) gap junctions, (2) tight junctions, (3) adherent junctions, (4) focal adhesion, and (5) regulation of actin cytoskeleton. In the thesis, we confirmed the presence of detected single nucleotide polymorphisms by comparing a large number of samples of pure marble and brown trout. Genes with confirmed polymorphisms that strictly separate marble and brown trout were used for genotypization of different hybrids of the two species, which are characterized by very different pigment patterns. We proved that in hybrids between marble and brown trout, the connection between pigment pattern and genotype of at least one of the tested candidate genes, amotl2a, was clearly indicated.