Climate change and deforestation have figured among the main causes of the pollinators’ decline. Especially for bees, the resulting losses of genetic diversity might cause higher levels of nonviable diploid male production, compromising population survival. Herein we evaluate the impact of both climate change and genetic diversity on the present and future of the orchid bee Euglossa annectans Dressler, 1982. We estimated the frequency of diploid males in 359 individuals using eight microsatellite loci. We also build ecological niche models based on 71 occurrence points to project the environmental suitability over time from the past 21 Ka towards 2050 considering the IPCC – RCP 4.5 scenario. We confirmed a diploid male frequency in E. annectans 10-folds higher than any other report for orchid bee species. The niche models also indicate an average reduction of 45.12% in suitable areas for the last 21 Ka and 36.34% up to 2050. Considering the species trend to diploid male production and the projected reduction of suitable area, we strongly recommend connecting and monitoring relictual populations as a strategy to increase the species potential distribution area.