Honeybees are important for global biodiversity and food production, but their populations face mounting challenges from climate change-induced stressors. Recent reports of regional declines in bee populations have attracted considerable attention worldwide. However, climate change poses several stressors like changes in temperatures with increased pesticide exposure and the presence of pathogens that have severely threatened honeybees. Even though we cannot determine the exact effects of potential environmental changes in honeybees brought about by climate change, we do have a great body of data available that demonstrates the influence of environmental changes on honeybees. Isolation of the molecular impacts allows getting a more fundamental understanding regarding how climate change at the most fundamental biological level affects honey bees. At a molecular scale, insects like honeybees tend to react to environmental changes through changes in gene expression, function of proteins, and cellular pathways. Such responses may affect a variety of physiological processes, including metabolism, immune function, and reproductive success. Biomarkers of stress and adaptation at the population or ecological level are identified by looking at molecular responses. This review synthesizes existing knowledge of climate change in honeybees at the molecular level, highlighting the urgent need for research that addresses the direct, long-term impacts of climate change on these mechanisms. Advancing such understanding will help in strategy development to strengthen honeybee resilience, thereby ensuring its survival and ecosystem stability under increasingly climatically challenged pressure.