Monoamine transporters have roles to regulate the monoamine concentrations in synaptic clefts in the central nervous system and are the targets of antidepressants and psychostimulants. They include transporters for norepinephrine, dopamine and serotonin, which are encoded by the SLC6A2, SLC6A3, and SLC6A4 genes, respectivily. We sequenced the full lengths of the coding regions of these genes for dogs and identified four single nucleotide polymorphisms (SNPs) in SLC6A2 and four in SLC6A3. One SLC6A3 SNP was non-synonymous and caused an amino acid substitution from threonine to serine. The genotype frequencies of these polymorphisms differed significantly among five breeds with different behavioral traits, suggesting that novel SLC6A2 and SLC6A3 SNPs would provide additional useful information for behavioral genetic studies in dogs.