Understanding how ecosystem disturbances affect biodiversity is difficult because communities contain many species each with unique traits that determine how communities as a whole respond to change. To address this problem posed by many diverse species, we take a phylogenetic approach when measuring the effect of ecosystem disturbance on biodiversity. Closely related species are more likely to share a broad range of traits and thus should have similar sensitivities to various environmental disturbances. Communities undergoing a disturbance should therefore be composed of a suite of closely related species that are able to withstand the disturbance. To test this hypothesis we used zooplankton community data from 18 whole-lake experiments. We found, on average, that these zooplankton communities contained more closely related species during the manipulations than before the manipulations. Control lake communities showed no such change. Communities that experienced abiotic manipulations (e.g., acidification) showed a stronger trend towards increased relatedness than did communities that experienced biotic manipulations (e.g., predator invasion). Thus, our analyses demonstrate that disturbance, regardless of the type, may generally skew the underlying phylogenetic component of biodiversity.