Morphological analysis of three-spined stickleback Gasterosteus aculeatus collected in Middleton Island, Alaska, was conducted in order to study how gene flow and selection interact during divergence. Middleton Island was uplifted by 3.4 m during the Great Alaska Earthquake in 1964; this event formed a series of new freshwater sites, triggering rapid evolution, and probably rapid speciation, in G. aculeatus populations that colonized them. The level of hybridization between the anadromous and the resident freshwater populations is reflected by the level of morphological variance of the resident freshwater G. aculeatus. Therefore, geographic isolation of the sites from the sea (approximating gene flow) and ionic concentration of the water (reflecting selection pressures) were correlated with morphological variance of the resident freshwater populations. Geographic isolation was negatively correlated with morphological variance in a majority of the analysed traits. Both selection and gene flow surrogates were found to be important influences on variance in morphology, though selection had a larger effect, especially on armour traits. It was concluded that gene flow appeared to constrain ecological speciation, but even in the presence of gene flow the strong selection in the freshwater environment was apparently leading to rapid divergence.