It is well known that speciation can often be fueled by the presence of ancestral variation that remains polymorphic in the present population. How the standing genetic variation (SGV) contributes to the rapid speciation in North American three-spined stickleback (Gasterosteus aculeatus) has been purposed previously by the transporter hypothesis. This hypothesis postulates that the ancestral freshwater alleles have been maintained in the marine stickleback populations by a migration-selection balance and serve as SGV to promote the invasion from marine to freshwater environment. By digging into the genomes of sticklebacks, I am interested in finding the supposed-to-be-rare freshwater alleles in the marine stickleback population in North America. Further tests taking advantages of population genetic tools and computer simulations will allow me to test if the “transporter” is truly the main driver behind the curious rapid speciation of three-spined stickleback.