The impact of accelerated climate change on extinction risk is not well-characterised despite its increasing relevance. Comparative genomics of extinct versus extant species might be useful in elucidating broad trends in faunal endangerment. We investigated fluctuations in genetic diversity and extinction timing in our genomic dataset of nine species of particularly vulnerable migratory shorebirds (Numenius), including two species widely thought to be extinct. Most species faced generally sharp declines in effective population sizes, a proxy for genetic diversity, soon after the Last Glacial Maximum. During this time, a warming climate supported forest expansions at the expense of open habitats, exacerbated by human-induced mass extinctions of megafauna only a few thousand years prior, resulting in unprecedented reductions in shorebird breeding habitat. Species breeding in temperate regions, where they widely overlap with human populations, have been most strongly affected. Late Quaternary events can exert long-lasting effects on some species' susceptibility to extinction. Genomic inquiry is crucial in informing conservation actions in the fight against ongoing biodiversity loss.