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Given the decline of pollinators around the world, preserving these animals has become a priority. This is especially urgent in threatened areas that concentrate high biodiversity such as the Atlantic forest (AF) in South America. Orchid bees are among the most important pollinators in the AF and are considered as good biological indicators of environmental quality. However, the populations of these bees have been reduced in size as a result of environmental impacts caused by human activities. In the present study, we used historical climate modelling to infer the refuge areas within the AF that concentrate high genetic diversity of orchid bees. From a total of 235 records of ten species, we built species models for the current days, Mid-Holocene and Last Glacial Maximum periods using MaxEnt program. Our results show refuge areas separately for each species, which may harbor their high levels of individual genetic diversity in the AF. On the other hand, the assemblage-scale model of climate stability shows a large continuous range of suitable areas from the southern to the northern AF, divided into three main stability zones (northeastern, central and southeastern-southern) where putatively are concentrated high levels of genetic diversity for most of these bees. This inference of stability zones should be useful to direct the choice of new conservation units in the AF, mainly in the northern portion of the AF, where the zone of greater suitability for orchid bees analyzed is present, which has been under protected and has experienced an increase of deforestation in the recent years. Finally, we point out that phylogeographic studies with these bees are necessary and might validate our findings.