Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly regarded as chance events and, as such, reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridizations, climate, land-use, and field-validated species distribution models, for two deeply divergent, naturally sympatric, and occasionally interbreeding toad species in Europe, belonging to the Bufo bufo and Bufotes viridis species groups. We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future.