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Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis (Bd) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd‐associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low‐occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family …