The emergence of new habitats is one of the largest events driving rapid phenotypic diversifications. After colonization of new habitats, populations will experience bottlenecks, so it remains unclear how such populations can rapidly change phenotypes and adapt to new environments. To address this question, we are investigating the ecological and genetic mechanisms underlying rapid phenotypic diversification in stickleback populations (genus Gasterosteus) newly created by the 2011 Tohoku earthquake and tsunamis. Our morphological analysis revealed that gill raker, an important trophic trait in fish, diversified among the new habitats only within three years. We next examined whether any ecological or genetic factors are associated with this phenotypic diversification. First, environmental surveys revealed that the new habitats varied in salinity and the density of benthos. We found significant effects of environmental variables on the gill raker number. Next, population genomic analyses showed that these new populations contained hybrids between freshwater G. aculeatus with fewer gill rakers and anadromous G. nipponicus with more gill rakers. Fish with higher gill raker numbers had higher proportions of genome derived from G. nipponicus. These results suggest that the hybridization between two distinct species may allow rapid phenotypic diversification and facilitate adaptation to new environments.