The undeniable environmental benefits of wind energy are undermined by the negative effects of wind farms on bird populations through mortality by collision with the energy-generating structures. Studies have documented morphological, ecological, and behavioral traits associated with vulnerability to wind turbines. However, practically all studies have concentrated on the effects on particular populations, and community-level analyses are lacking. Here we assess the susceptibility of species on the basis of their morphology, and examine the effect of selective mortality on the topology and dispersion of phylogenies, and on the structure and volume of the ecological morphospace of bird assemblages. Using an extensive database of bird occurrences and fatalities in a wind farm located in southern Mexico, and performing null models to establish statistical significance, we compared sets of affected and unaffected species in terms of their wing morphology and position in a phylogeny. We found that birds more likely to fly in the risk zone tend to be smaller, with longer wings, and with heavier wing loadings. Within this group, species more likely to collide with blades and die are smaller, with short wings, and supporting lighter wing loadings. These patterns determine that the set of species less affected distribute in morphospace leaving noticeable holes (morphologies not represented). Birds flying in the risk zone tend to be related to each other, but species that actually collide with turbines belong to several separate clades. These differential effects on morphology and phylogenetic diversity pose important and complex challenges to the conservation of birds in areas where wind farms are being established.