Differences in behavior of domesticated animals from their wild ancestors provide one of the best examples of the influence of genes on behavior but the identification of the underlying genes has been proved to be extremely difficult. Unlike the species, which were domesticated historically and selected for many different traits including morphology and appearance, the red fox (Vulpes vulpes) was domesticated in a controlled experiment by selection solely for behavior. The fox model may therefore provide advantages for the identification of genes implicated in domesticated behavior. We sequenced and assembled the genome of the red fox and re-sequenced a subset of foxes from domesticated population, population selected for aggressive behavior, and conventional farm-bred population to identify genomic regions associated with selection for behavior. The sequence analysis identified 30 regions of reduced heterozygosity in domesticated population and 34 regions of extreme divergence between domesticated and other fox populations, 13 identified regions overlapped between the two analyses. The nonsynonymous substitutions were identified in several genes located in identified regions including genes involved in synaptic plasticity and signal transduction. One region contained a single gene, SorCS1, a trafficking regulator of neurexin and AMPA receptors. The effect of this gene on behavior was confirmed using fox experimental three-generation pedigrees constructed by breeding domesticated foxes and foxes selected for aggressive behavior. The analysis of the fox brain transcriptome suggested the effect of SorCS1 genotypes on gene expression. The fox findings may be further validated in dogs and may help to shed light on the intriguing question of whether domesticated behavior in different species is regulated through similar gene networks.