Global warming is an environmental phenomenon to which species must adapt to survive. Drosophila subobscura presents an adaptive capacity due to its chromosomal inversion polymorphism. Until now, the impact of global warming on this polymorphism has been studied in D. subobscura populations located either on a continental mainland or on islands not far from a continent. In this context, gene flow could be a relevant mechanism allowing the movement of thermally adapted inversions between populations. Our aim was to sample and study the chromosomal polymorphism on Madeira, a small isolated island in the Atlantic Ocean. We compared our findings with those reported in the same location approximately four and five decades ago. Moreover, we studied whether global warming has occurred on this island by analyzing mean, maximum and minimum temperatures over a 55‐year period. All atmospheric parameters have increased significantly, consistent with climate change expectations. Frequencies and chromosomal thermal index values of thermal adapted inversions remained quite stable over years. Furthermore, J, U and O chromosomes are almost fixed for “warm” adapted inversions. Thus, if there is little genetic variability remaining and temperatures continue increasing, island populations of D. subobscura might be on the threshold of endangerment. However, apart from selection, genetic drift and inbreeding, other processes, such as phenotypic plasticity or thermoregulatory behavior, could be involved in the survival of the species’ populations. Finally, although in danger, D. subobscura is a generalist that lives in humanized environments, and this fact could favor its persistence on Madeira Island.