Genetic variability is essential for adaptation and isolated populations lacking variability can face extinction when environments change. A currently underappreciated source of genetic variability is hybridization with a closely related lineage. Hybridization can indeed facilitate adaptation e.g. via exchange of adaptive genetic material between species. Here we investigate the potential role of temperature in shaping the genetic variability in a hybrid population between Formica polyctena and F. aquilonia wood ants using long term population genetic data. We find that the frequencies of both parental-like alleles in the hybrid population co-vary with temperature over the years in males but not in females. Results suggest hybridization can lead to sex-specific outcomes that are dependent on ecological factors and that genetic variability resulting from hybridization could help hybrids cope with varying temperature.