Population models are based upon the ideology that removing large, old individuals provides space for young, fast-growing counterparts that can maximize (fisheries) yields while maintaining population and ecosystem stability. Yet, we revealed that compensatory density dependence only existed for 49% of target coral-reef fishes exposed to growing fishing pressure across Pacific islands. Remaining species slowly disappeared from landings and reefs with limited population replenishment. To understand these remarkable differences, we constructed phylogenies for dominant fish families and discovered that large patristic distances between sister species, or greater isolation, predicted size-and-age truncation. Isolated species appeared to have greater niche dominance or breadth, supported by their faster growth rates and group foraging behavior. In contrast, closely related species may have more restricted, realized niches that led to their disappearance and replacement. Phylogenetic attributes offered novel guidance to proactively manage multispecies fisheries and improve our understanding of ecological niches and ecosystem stability.