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Cryptic species represent a large component of hidden biodiversity. Some cryptic taxa require specific climate and habitat conditions and have limited dispersal abilities. In order to assess the importance of cryptic species and to minimize future loss of biodiversity, we modelled the current and future distribution of the Merodon atratus (Oldenberg, 1919) species complex, once thought to be a single species, and compared it with species distribution models for each of the three cryptic species within the complex (M. atratus, M. balkanicus Sai, Aanski et Vuji, 2016, M. virgatus Vuji et Radenkovi, 2016). Additionally, we compared environmental niche models for each cryptic species. We then tested the capability of nationally designated protected areas to encompass the species complex and each cryptic species of the complex. We conclude that although cryptic species of the M. atratus complex exhibit high levels of morphological similarity, they will respond differently to global climate change, requiring tailored particular conservation strategies. Overall, the species complex will drastically decrease its range and retreat to the Alps. More specifically, each cryptic species requires specific environmental conditions and will react differently to climate change. These results contribute to the establishment of a conservation status for these newly discovered species and their conservation management, particularly for M. balkanicus that is projected to go extinct due to global warming.