Middleton Island, Alaska, had undergone substantial tectonic uplift during the Great Alaska Earthquake of 1964, which caused the formation of a new marine terrace around the island. This terrace holds a large number of new-formed freshwater sites. Threespine stickleback were collected from 18 sites, and anadromous—resident-freshwater species pairs were found in five of the sites. Geographic conditions in Middleton Island do not favor the possibility of independent colonization of the newformed sites by an existing, pre-1964 resident-freshwater population. Significant morphological differences between allopatric anadromous and resident-freshwater populations therefore demonstrate that colonization was followed by rapid evolution toward the resident-freshwater phenotype. Significant differences between sympatric species pairs indicate reproductive isolation and suggest rapid speciation. Further analyses indicate that this rapid speciation is constrained by gene flow, and that it reflects a balance between selection and gene flow, in which selection seems to have a stronger effect on the final outcome.