Biologists have long sought to understand the evolutionary dynamics of island community assembly, and the study of remote island biotas has been particularly informative for generating and testing theoretical frameworks. While reconstructing the dynamics of colonization and post-colonization evolutionary changes has long been a challenge, emerging next-generation technologies for molecular and morphological analysis offer new data streams that can be brought to bear on the problem. Here, we examined the evolutionary assembly of ant community in the Fijian archipelago by integrating the “community genomics” approach and x-ray microtomography/3D morphometrics in a comparative framework. We find that the highly endemic Fijian ant fauna was assembled through a series of colonizations and radiations over millions of years, followed by more recent arrivals of regionally widespread and alien species from outside the region. Within the radiations of those highly endemic species, we observed a strong ecomorphological diversification and the subsequent ecological niche shift. Using demographic modeling, we show that the vast majority of endemic species are in decline, while the population of non-endemic species are expansion. Taken together, this study advances our knowledge of community assembly by unraveling the evolutionary assembly of Fijian ants.