Studies of the fossil record can inform our understanding of not only the causes of mass extinctions, but also their effects on biodiversity, ecology and evolution. Here, we examine regional-scale ecological changes resulting from a Late Devonian mass extinction event using brachiopod fossil assemblages from the Appalachian Basin. About half of the species went extinct, but were largely replaced by new immigrant taxa. Both before and after the extinction, the primary gradient in faunal composition was correlated with onshore-offshore position, with a second gradient attributed to frequency of disturbance. Survivors of the extinction displayed a strong degree of niche conservatism along these gradients. Despite these indicators of ecological stability, the pre- and post-extinction faunas were quite distinct at the order level, with atrypids and strophomenids largely replaced by productids, whose spiny shells may have provided greater resistance to disturbance and/or predation. Thus, extinction survivors persisted in similar ecological niches despite environmental perturbations and considerable change in the taxonomic and ecological composition of the regional species pool.