Extinctions are caused by environmental and ecological change but are recognized and measured in the fossil record by the disappearance of clades or lineages. If the ecological preferences of lineages or taxa are weakly congruent with their phylogenetic relationships, even large ecological perturbations are unlikely to drive major clades extinct because the factors that eliminate some species are unlikely to affect close relatives with different ecological preferences. In contrast, if phylogenetic relatedness and ecological preferences are congruent, then ecological perturbations can more easily cause extinctions of large clades. In order to quantify this effect, we used a computer model to simulate the diversification and extinction of clades based on ecological criteria. By varying the parameters of the model, we explored (1) the relationship between the extinction probability for a clade of a given size (number of terminals) and the overall intensity of extinction (the proportion of the terminals that go extinct), and (2) the congruence between ecological traits of the terminals and their phylogenetic relationships. Data from two extinctions (planktonic foraminifera at the Eocene/Oligocene boundary and vascular land plants at the Middle/Late Pennsylvanian boundary) show phylogenetic clustering of both ecological traits and extinction probability and demonstrate the interaction of these factors. The disappearance of large clades is observed in the fossil record, but our model suggests that it is very improbable without both high overall extinction intensities and high congruence between ecology and phylogeny.