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A worldwide decline of many bee species has been reported, but conversely some species seems to be in expansion. Nonetheless species truly in expansion may be overestimated, especially when they are considered as a whole, and information about intraspecific lineages is lacking. The objective of this study was to test whether the bumblebee species Bombus morio and B. pauloensis will be safe under future climate changes. Specifically, test if these bees will suffer geographic decline or expansion; test whether each phylogeographic lineage within B. pauloensis will respond differently in modeling of future geographic distribution given climate change; find stable areas holding high genetic diversity based on predicted future climatic changes; and test whether these areas are covered by existing protected areas. To reach the objectives we performed analyses using phylogeographic data already available and climate change information to model the demography of the panmictic B. morio and the phylogeographic lineages in B. pauloensis. Our results suggest that both species will suffer a reduction in suitable area and that the reduction in distribution is masked for B. pauloensis. When each clade was separately analyzed, the ones in the edge of the species distribution are the most likely to decline. We found a large future refuge in eastern state of SAo Paulo and state of Rio de Janeiro for B. morio and for the clades of B. pauloensis. This refuge seems to show high levels of species richness and endemism for different taxa. Thus, by protecting this area we will be preserving not only the pattern of biodiversity but also the processes that generate and maintain them for many other species.