Evolutionary history is expected to play a major role in determining which species decline in population size to extinction in response to environmental change, but the processes by which this comes about are poorly understood. In particular, although many studies have identified broad-scale biological correlates of extinction risk, the population-scale processes driving such macro-ecological and macro-evolutionary patterns are usually hypotheses that remain to be tested. Although population genetic studies provide much promise to understand the micro-evolutionary processes underlying such patterns of extinction risk, inferences can be limited by our confidence in the timescales inferred, and by the scale of such studies, which frequently include only one lineage. Furthermore, comparisons across studies are frequently confounded by case-specific differences in exposure to environmental change. Here we tackle all three of these issues, applying ancient DNA methods to historical museum samples and subfossils to obtain a genome-wide time series for eight Mascarene island bird lineages that differ in abundance and other biological traits. Islands of the Mascarene archipelago, Indian Ocean, are unusual among sizable and biologically diverse landmasses worldwide, in that they had no human population until European arrival 400 years ago. Therefore, there exist museum samples and subfossils spanning the full duration of environmental change. As a consequence, we will obtain what is to our knowledge, the first real time assessment of genetic response to anthropogenic environmental change across multiple species following first human presence. Our study setup involves four separate cases in which the effects of common environmental change can be compared between a pair of sympatric and closely related species on the same island that differ in abundance (a “rare” species versus a “common” one). By considering common environmental change of well-known duration, our project provides a rare opportunity to dissect the contribution of evolutionary biology and ecology (i.e. susceptibility) in determining which species are threatened with extinction. This includes assessing the relative contribution of a species’ evolutionary past (species differing in degree of ecological specialisation, time in situ, trophic level, genetic diversity), versus evolution in action (selection), in defining demographic trajectories.